Mercurial > repos > geert-vandeweyer > varscan_wrapper
changeset 1:e5831cc9185f draft
Deleted selected files
| author | geert-vandeweyer |
|---|---|
| date | Fri, 07 Mar 2014 06:18:01 -0500 |
| parents | 848f3dc54593 |
| children | 90c9b7a6e58b |
| files | varscan/output.validation varscan/tool_dependencies.xml varscan/varscan_mpileup.pl varscan/varscan_mpileup.xml varscan/varscan_processSomatic.pl varscan/varscan_processSomatic.xml varscan/varscan_somatic.native.xml varscan/varscan_somatic.pl varscan/varscan_somatic.xml |
| diffstat | 9 files changed, 0 insertions(+), 1534 deletions(-) [+] |
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--- a/varscan/output.validation Fri Mar 07 06:17:32 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,441 +0,0 @@ -##fileformat=VCFv4.1 -##source=VarScan2 -##INFO=<ID=DP,Number=1,Type=Integer,Description="Total depth of quality bases"> -##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Indicates if record is a somatic mutation"> -##INFO=<ID=SS,Number=1,Type=String,Description="Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)"> -##INFO=<ID=SSC,Number=1,Type=String,Description="Somatic score in Phred scale (0-255) derived from somatic p-value"> -##INFO=<ID=GPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls"> -##INFO=<ID=SPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls"> -##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand"> -##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position"> -##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> -##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> -##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> -##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)"> -##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)"> -##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency"> -##FORMAT=<ID=DP4,Number=1,Type=String,Description="Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev"> -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR -chr1 11190596 . T . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:13,7,0,0 0/0:.:8:8:0:0%:6,2,0,0 -chr1 11190597 . T . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:13,7,0,0 0/0:.:8:8:0:0%:6,2,0,0 -chr1 11190598 . C . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:13,7,0,0 0/0:.:8:7:0:0%:5,2,0,0 -chr1 11190599 . T . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:13,7,0,0 0/0:.:8:7:0:0%:6,1,0,0 -chr1 11190600 . T . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:13,7,0,0 0/0:.:8:7:0:0%:5,2,0,0 -chr1 11190601 . C . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:13,7,0,0 0/0:.:8:8:0:0%:6,2,0,0 -chr1 11190602 . T . PASS DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:21:19:0:0%:13,6,0,0 0/0:.:11:8:0:0%:6,2,0,0 -chr1 11190603 . G . PASS DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:21:20:0:0%:14,6,0,0 0/0:.:11:11:0:0%:9,2,0,0 -chr1 11190604 . C . PASS DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:21:20:0:0%:13,7,0,0 0/0:.:13:12:0:0%:8,4,0,0 -chr1 11190605 . A . PASS DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:21:20:0:0%:13,7,0,0 0/0:.:13:10:0:0%:8,2,0,0 -chr1 11190606 . G . PASS DP=36;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:22:20:0:0%:13,7,0,0 0/0:.:14:12:0:0%:8,4,0,0 -chr1 11190607 . C . PASS DP=36;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:22:22:0:0%:13,9,0,0 0/0:.:14:14:0:0%:9,5,0,0 -chr1 11190608 . G . PASS DP=36;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:22:22:0:0%:13,9,0,0 0/0:.:14:12:0:0%:7,5,0,0 -chr1 11190609 . G . PASS DP=37;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:22:22:0:0%:13,9,0,0 0/0:.:15:14:0:0%:9,5,0,0 -chr1 11190610 . C . PASS DP=37;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:22:22:0:0%:13,9,0,0 0/0:.:15:15:0:0%:9,6,0,0 -chr1 11190611 . G . PASS DP=37;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:22:21:0:0%:13,8,0,0 0/0:.:15:15:0:0%:9,6,0,0 -chr1 11190612 . A . PASS DP=38;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:23:21:0:0%:13,8,0,0 0/0:.:15:13:0:0%:8,5,0,0 -chr1 11190613 . T . PASS DP=39;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:24:24:0:0%:13,11,0,0 0/0:.:15:14:0:0%:8,6,0,0 -chr1 11190614 . G . PASS DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:25:25:0:0%:13,12,0,0 0/0:.:15:15:0:0%:9,6,0,0 -chr1 11190615 . G . PASS DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:25:25:0:0%:13,12,0,0 0/0:.:15:15:0:0%:9,6,0,0 -chr1 11190616 . G . PASS DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:25:25:0:0%:13,12,0,0 0/0:.:15:15:0:0%:9,6,0,0 -chr1 11190617 . G . PASS DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:25:24:0:0%:13,11,0,0 0/0:.:15:15:0:0%:9,6,0,0 -chr1 11190618 . T . PASS DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:25:24:0:0%:12,12,0,0 0/0:.:15:13:0:0%:8,5,0,0 -chr1 11190619 . G . PASS DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:25:25:0:0%:13,12,0,0 0/0:.:15:15:0:0%:9,6,0,0 -chr1 11190620 . G . PASS DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:25:24:0:0%:13,11,0,0 0/0:.:15:15:0:0%:9,6,0,0 -chr1 11190621 . G . PASS DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:25:25:0:0%:13,12,0,0 0/0:.:15:14:0:0%:8,6,0,0 -chr1 11190622 . G . PASS DP=41;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:25:24:0:0%:13,11,0,0 0/0:.:16:14:0:0%:8,6,0,0 -chr1 11190623 . C . PASS DP=42;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:25:24:0:0%:12,12,0,0 0/0:.:17:17:0:0%:9,8,0,0 -chr1 11190624 . T . PASS DP=42;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:25:25:0:0%:13,12,0,0 0/0:.:17:17:0:0%:9,8,0,0 -chr1 11190625 . G . PASS DP=42;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:25:25:0:0%:13,12,0,0 0/0:.:17:17:0:0%:9,8,0,0 -chr1 11190626 . T . PASS DP=42;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:25:25:0:0%:13,12,0,0 0/0:.:17:17:0:0%:9,8,0,0 -chr1 11190627 . T . PASS DP=42;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:25:23:0:0%:11,12,0,0 0/0:.:17:16:0:0%:8,8,0,0 -chr1 11190628 . C . PASS DP=42;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:25:25:0:0%:13,12,0,0 0/0:.:17:16:0:0%:9,7,0,0 -chr1 11190629 . T . PASS DP=42;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:25:25:0:0%:13,12,0,0 0/0:.:17:16:0:0%:9,7,0,0 -chr1 11190630 . C . PASS DP=41;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:25:25:0:0%:13,12,0,0 0/0:.:16:16:0:0%:9,7,0,0 -chr1 11190631 . G . PASS DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:25:25:0:0%:13,12,0,0 0/0:.:15:15:0:0%:8,7,0,0 -chr1 11190632 . G . PASS DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:25:25:0:0%:13,12,0,0 0/0:.:15:15:0:0%:8,7,0,0 -chr1 11190633 . T . PASS DP=42;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:27:24:0:0%:11,13,0,0 0/0:.:15:15:0:0%:8,7,0,0 -chr1 11190634 . G . PASS DP=42;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:27:26:0:0%:14,12,0,0 0/0:.:15:14:0:0%:8,6,0,0 -chr1 11190635 . C . PASS DP=42;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:27:27:0:0%:14,13,0,0 0/0:.:15:14:0:0%:7,7,0,0 -chr1 11190636 . T . PASS DP=42;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:27:26:0:0%:13,13,0,0 0/0:.:15:14:0:0%:7,7,0,0 -chr1 11190637 . C . PASS DP=41;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:27:26:0:0%:13,13,0,0 0/0:.:14:14:0:0%:7,7,0,0 -chr1 11190638 . T . PASS DP=41;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:27:27:0:0%:14,13,0,0 0/0:.:14:14:0:0%:7,7,0,0 -chr1 11190639 . C . PASS DP=41;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:27:27:0:0%:14,13,0,0 0/0:.:14:14:0:0%:7,7,0,0 -chr1 11190640 . G . PASS DP=41;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:27:26:0:0%:13,13,0,0 0/0:.:14:14:0:0%:7,7,0,0 -chr1 11190641 . G . PASS DP=41;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:27:27:0:0%:14,13,0,0 0/0:.:14:14:0:0%:7,7,0,0 -chr1 11190642 . C . PASS DP=46;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:27:27:0:0%:15,12,0,0 0/0:.:19:16:0:0%:9,7,0,0 -chr1 11190643 . C . PASS DP=50;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:29:29:0:0%:15,14,0,0 0/0:.:21:19:0:0%:10,9,0,0 -chr1 11190644 . T . PASS DP=51;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:30:30:0:0%:15,15,0,0 0/0:.:21:21:0:0%:12,9,0,0 -chr1 11190645 . C . PASS DP=52;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:30:29:0:0%:15,14,0,0 0/0:.:22:21:0:0%:12,9,0,0 -chr1 11190646 . G A . PASS DP=53;SOMATIC;SS=2;SSC=13;GPV=1E0;SPV=4.429E-2 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:31:31:0:0%:15,16,0,0 0/1:.:22:15:3:16.67%:9,6,1,2 -chr1 11190647 . C . PASS DP=53;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:31:29:0:0%:13,16,0,0 0/0:.:22:20:0:0%:10,10,0,0 -chr1 11190648 . T . PASS DP=53;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:31:31:0:0%:15,16,0,0 0/0:.:22:20:0:0%:10,10,0,0 -chr1 11190649 . C . PASS DP=53;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:31:31:0:0%:15,16,0,0 0/0:.:22:22:0:0%:12,10,0,0 -chr1 11190650 . T . PASS DP=53;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:31:31:0:0%:15,16,0,0 0/0:.:22:22:0:0%:12,10,0,0 -chr1 11190651 . C . PASS DP=53;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:30:30:0:0%:14,16,0,0 0/0:.:23:21:0:0%:11,10,0,0 -chr1 11190652 . A . PASS DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:21:19:0:0%:10,9,0,0 0/0:.:19:17:0:0%:9,8,0,0 -chr1 11190653 . C . PASS DP=37;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:18:17:0:0%:7,10,0,0 0/0:.:19:19:0:0%:9,10,0,0 -chr1 11190654 . T . PASS DP=37;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:18:18:0:0%:8,10,0,0 0/0:.:19:17:0:0%:9,8,0,0 -chr1 11190655 . G . PASS DP=30;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:16:15:0:0%:7,8,0,0 0/0:.:14:14:0:0%:6,8,0,0 -chr1 11190656 . T . PASS DP=30;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:16:15:0:0%:6,9,0,0 0/0:.:14:14:0:0%:6,8,0,0 -chr1 11190657 . T . PASS DP=30;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:16:15:0:0%:6,9,0,0 0/0:.:14:13:0:0%:5,8,0,0 -chr1 11190658 . G . PASS DP=30;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:16:15:0:0%:7,8,0,0 0/0:.:14:14:0:0%:6,8,0,0 -chr1 11190659 . C . PASS DP=30;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:16:14:0:0%:5,9,0,0 0/0:.:14:13:0:0%:6,7,0,0 -chr1 11190660 . T . PASS DP=31;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:17:17:0:0%:7,10,0,0 0/0:.:14:14:0:0%:6,8,0,0 -chr1 11190661 . G . PASS DP=31;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:17:16:0:0%:7,9,0,0 0/0:.:14:14:0:0%:6,8,0,0 -chr1 11190662 . C . PASS DP=31;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:17:16:0:0%:6,10,0,0 0/0:.:14:14:0:0%:6,8,0,0 -chr1 11190663 . C . PASS DP=31;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:17:17:0:0%:7,10,0,0 0/0:.:14:14:0:0%:6,8,0,0 -chr1 11190664 . C . PASS DP=31;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:17:15:0:0%:6,9,0,0 0/0:.:14:14:0:0%:6,8,0,0 -chr1 11190665 . T . PASS DP=31;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:17:16:0:0%:7,9,0,0 0/0:.:14:8:0:0%:4,4,0,0 -chr1 11190666 . C . PASS DP=31;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:17:16:0:0%:7,9,0,0 0/0:.:14:12:0:0%:6,6,0,0 -chr1 11190667 . G . PASS DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:17:16:0:0%:7,9,0,0 1/1:.:15:15:0:0%:6,9,0,0 -chr1 11190668 . G . PASS DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:17:16:0:0%:7,9,0,0 1/1:.:15:15:0:0%:6,9,0,0 -chr1 11190669 . T A . str10 DP=32;SS=0;SSC=0;GPV=1E0;SPV=4.8148E-1 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:17:14:0:0%:5,9,0,0 1/1:.:15:12:1:7.69%:4,8,1,0 -chr1 11190670 . G . PASS DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:17:14:0:0%:6,8,0,0 1/1:.:15:10:0:0%:5,5,0,0 -chr1 11190671 . C . PASS DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:17:15:0:0%:5,10,0,0 1/1:.:15:14:0:0%:6,8,0,0 -chr1 11190672 . T . PASS DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:17:17:0:0%:7,10,0,0 1/1:.:15:15:0:0%:6,9,0,0 -chr1 11190673 . G . PASS DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:17:17:0:0%:7,10,0,0 1/1:.:15:13:0:0%:5,8,0,0 -chr1 11190674 . G . PASS DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:17:13:0:0%:7,6,0,0 1/1:.:15:15:0:0%:6,9,0,0 -chr1 11190675 . C . PASS DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:17:15:0:0%:5,10,0,0 1/1:.:15:14:0:0%:5,9,0,0 -chr1 11190676 . A . PASS DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:17:15:0:0%:6,9,0,0 1/1:.:15:14:0:0%:5,9,0,0 -chr1 11190677 . G . PASS DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:17:17:0:0%:7,10,0,0 1/1:.:15:15:0:0%:6,9,0,0 -chr1 11190678 . T . PASS DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:17:13:0:0%:5,8,0,0 1/1:.:15:15:0:0%:6,9,0,0 -chr1 11190679 . G . PASS DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:17:17:0:0%:7,10,0,0 1/1:.:15:14:0:0%:6,8,0,0 -chr1 11190680 . G . PASS DP=31;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:16:16:0:0%:7,9,0,0 1/1:.:15:15:0:0%:6,9,0,0 -chr1 11190681 . T . PASS DP=31;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:16:16:0:0%:7,9,0,0 1/1:.:15:15:0:0%:6,9,0,0 -chr1 11190682 . G . PASS DP=31;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:16:16:0:0%:7,9,0,0 1/1:.:15:13:0:0%:6,7,0,0 -chr1 11190683 . G . PASS DP=31;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:16:16:0:0%:7,9,0,0 1/1:.:15:14:0:0%:6,8,0,0 -chr1 11190684 . T . PASS DP=30;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:16:14:0:0%:5,9,0,0 1/1:.:14:13:0:0%:4,9,0,0 -chr1 11190685 . G . PASS DP=30;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:16:16:0:0%:7,9,0,0 1/1:.:14:14:0:0%:5,9,0,0 -chr1 11190686 . G . PASS DP=30;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:16:16:0:0%:7,9,0,0 1/1:.:14:12:0:0%:5,7,0,0 -chr1 11190687 . C . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:16:15:0:0%:6,9,0,0 1/1:.:12:11:0:0%:3,8,0,0 -chr1 11190688 . A . PASS DP=27;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:15:15:0:0%:6,9,0,0 1/1:.:12:12:0:0%:4,8,0,0 -chr1 11190689 . G . PASS DP=27;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:15:15:0:0%:6,9,0,0 1/1:.:12:11:0:0%:3,8,0,0 -chr1 11190690 . T . PASS DP=27;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:15:14:0:0%:5,9,0,0 1/1:.:12:10:0:0%:4,6,0,0 -chr1 11190691 . G . PASS DP=26;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:14:14:0:0%:5,9,0,0 1/1:.:12:12:0:0%:4,8,0,0 -chr1 11190692 . G . PASS DP=26;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:14:13:0:0%:5,8,0,0 1/1:.:12:11:0:0%:4,7,0,0 -chr1 11190693 . C . PASS DP=25;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:14:13:0:0%:4,9,0,0 1/1:.:11:9:0:0%:3,6,0,0 -chr1 11190694 . G . PASS DP=25;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:14:13:0:0%:4,9,0,0 1/1:.:11:9:0:0%:2,7,0,0 -chr1 11190695 . G . PASS DP=23;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:12:12:0:0%:3,9,0,0 1/1:.:11:11:0:0%:3,8,0,0 -chr1 11319318 . A . PASS DP=21;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:12:12:0:0%:7,5,0,0 0/0:.:9:6:0:0%:4,2,0,0 -chr1 11319319 . T . PASS DP=21;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:12:9:0:0%:4,5,0,0 0/0:.:9:9:0:0%:5,4,0,0 -chr1 11319320 . G . PASS DP=21;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:12:11:0:0%:7,4,0,0 0/0:.:9:9:0:0%:5,4,0,0 -chr1 11319321 . G . PASS DP=21;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:12:12:0:0%:8,4,0,0 0/0:.:9:9:0:0%:5,4,0,0 -chr1 11319322 . T G . PASS DP=22;SS=0;SSC=0;GPV=1E0;SPV=5E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:13:8:1:11.11%:5,3,0,1 0/0:.:9:9:0:0%:5,4,0,0 -chr1 11319323 . G . PASS DP=23;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:14:14:0:0%:9,5,0,0 0/0:.:9:8:0:0%:4,4,0,0 -chr1 11319324 . A . PASS DP=23;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:14:14:0:0%:9,5,0,0 0/0:.:9:9:0:0%:5,4,0,0 -chr1 11319325 . C . PASS DP=23;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:14:13:0:0%:8,5,0,0 0/0:.:9:9:0:0%:5,4,0,0 -chr1 11319326 . A . PASS DP=23;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:14:14:0:0%:9,5,0,0 0/0:.:9:9:0:0%:5,4,0,0 -chr1 11319327 . T . PASS DP=23;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:14:12:0:0%:7,5,0,0 0/0:.:9:7:0:0%:5,2,0,0 -chr1 11319328 . A . PASS DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:15:15:0:0%:9,6,0,0 0/0:.:9:9:0:0%:5,4,0,0 -chr1 11319329 . G . PASS DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:15:14:0:0%:8,6,0,0 0/0:.:9:7:0:0%:5,2,0,0 -chr1 11319330 . T . PASS DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:15:15:0:0%:9,6,0,0 0/0:.:9:9:0:0%:5,4,0,0 -chr1 11319331 . G . PASS DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:15:14:0:0%:9,5,0,0 0/0:.:9:7:0:0%:5,2,0,0 -chr1 11319332 . C . PASS DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:15:15:0:0%:9,6,0,0 0/0:.:9:7:0:0%:5,2,0,0 -chr1 11319333 . T . PASS DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:15:13:0:0%:7,6,0,0 0/0:.:9:9:0:0%:5,4,0,0 -chr1 11319334 . G . PASS DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:15:15:0:0%:9,6,0,0 0/0:.:9:9:0:0%:5,4,0,0 -chr1 11319335 . G . PASS DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:15:15:0:0%:9,6,0,0 0/0:.:9:9:0:0%:5,4,0,0 -chr1 45292432 . C . PASS DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:32:31:0:0%:14,17,0,0 0/0:.:8:7:0:0%:2,5,0,0 -chr1 45292433 . T . PASS DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:32:32:0:0%:15,17,0,0 0/0:.:8:7:0:0%:2,5,0,0 -chr1 45292434 . G . PASS DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:32:30:0:0%:15,15,0,0 0/0:.:8:8:0:0%:3,5,0,0 -chr1 45292435 . G C . PASS DP=40;SS=0;SSC=0;GPV=1E0;SPV=8.2051E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:32:31:1:3.12%:15,16,0,1 0/0:.:8:7:0:0%:3,4,0,0 -chr1 45292436 . C . PASS DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:32:30:0:0%:14,16,0,0 0/0:.:8:7:0:0%:3,4,0,0 -chr1 45292437 . G . PASS DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:32:32:0:0%:15,17,0,0 0/0:.:8:8:0:0%:3,5,0,0 -chr1 45292438 . G . PASS DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:32:32:0:0%:15,17,0,0 0/0:.:8:8:0:0%:3,5,0,0 -chr1 45292439 . G . PASS DP=40;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:32:32:0:0%:15,17,0,0 0/0:.:8:8:0:0%:3,5,0,0 -chr1 45292440 . A . PASS DP=38;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:30:28:0:0%:13,15,0,0 0/0:.:8:8:0:0%:3,5,0,0 -chr1 45292441 . C . PASS DP=38;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:30:28:0:0%:12,16,0,0 0/0:.:8:8:0:0%:3,5,0,0 -chr1 45292442 . T A . PASS DP=38;SS=0;SSC=0;GPV=1E0;SPV=8.3333E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:30:29:1:3.33%:13,16,1,0 0/0:.:8:6:0:0%:3,3,0,0 -chr1 45293099 . C . PASS DP=20;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:12:12:0:0%:6,6,0,0 0/0:.:8:7:0:0%:3,4,0,0 -chr1 45293100 . A . PASS DP=20;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:12:11:0:0%:5,6,0,0 0/0:.:8:5:0:0%:2,3,0,0 -chr1 45293101 . G . PASS DP=20;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:12:12:0:0%:6,6,0,0 0/0:.:8:6:0:0%:2,4,0,0 -chr1 45293102 . C . PASS DP=20;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:12:12:0:0%:6,6,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr1 45293103 . C . PASS DP=20;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:12:12:0:0%:6,6,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr1 45293104 . A . PASS DP=20;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:12:12:0:0%:6,6,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr1 45293105 . G . PASS DP=22;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:14:14:0:0%:6,8,0,0 0/0:.:8:7:0:0%:3,4,0,0 -chr1 45293106 . G . PASS DP=22;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:14:13:0:0%:6,7,0,0 0/0:.:8:7:0:0%:4,3,0,0 -chr1 45293107 . T . PASS DP=22;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:14:14:0:0%:6,8,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr1 45293108 . G . PASS DP=23;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:15:15:0:0%:6,9,0,0 0/0:.:8:6:0:0%:3,3,0,0 -chr1 45293109 . C C . str10 DP=23;SS=0;SSC=0;GPV=5.3885E-2;SPV=3.7799E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/1:.:15:13:2:13.33%:5,8,1,1 0/1:.:8:5:2:28.57%:3,2,0,2 -chr1 45293110 . G . PASS DP=23;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:15:14:0:0%:6,8,0,0 0/0:.:8:6:0:0%:2,4,0,0 -chr1 45293111 . G . PASS DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:16:16:0:0%:6,10,0,0 0/0:.:8:6:0:0%:2,4,0,0 -chr1 45293112 . G . PASS DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:16:16:0:0%:6,10,0,0 0/0:.:8:7:0:0%:3,4,0,0 -chr1 45293113 . G . PASS DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:16:15:0:0%:6,9,0,0 0/0:.:8:7:0:0%:3,4,0,0 -chr1 45293114 . T . PASS DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:16:15:0:0%:5,10,0,0 0/0:.:8:5:0:0%:1,4,0,0 -chr1 45293115 . G . PASS DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:16:15:0:0%:6,9,0,0 0/0:.:8:7:0:0%:3,4,0,0 -chr1 45293116 . C . PASS DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:16:15:0:0%:5,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr1 45293117 . C . PASS DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:16:16:0:0%:6,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr1 45293118 . T T . PASS DP=24;SS=0;SSC=0;GPV=5.4264E-2;SPV=4.3478E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/1:.:16:13:2:13.33%:4,9,1,1 0/1:.:8:6:2:25%:3,3,1,1 -chr1 45293119 . G . PASS DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:16:14:0:0%:5,9,0,0 0/0:.:8:6:0:0%:3,3,0,0 -chr1 45293120 . G . PASS DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:16:14:0:0%:5,9,0,0 0/0:.:8:6:0:0%:3,3,0,0 -chr1 45293121 . G . PASS DP=23;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:15:13:0:0%:4,9,0,0 0/0:.:8:6:0:0%:3,3,0,0 -chr1 45293122 . T . PASS DP=23;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:15:14:0:0%:5,9,0,0 0/0:.:8:7:0:0%:3,4,0,0 -chr1 45293123 . G . PASS DP=23;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:15:15:0:0%:5,10,0,0 0/0:.:8:6:0:0%:4,2,0,0 -chr1 45293124 . G . PASS DP=23;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:15:15:0:0%:5,10,0,0 0/0:.:8:7:0:0%:4,3,0,0 -chr1 45293284 . T . PASS DP=31;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:23:21:0:0%:10,11,0,0 0/0:.:8:6:0:0%:3,3,0,0 -chr1 45293285 . G . PASS DP=31;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:23:21:0:0%:12,9,0,0 0/0:.:8:7:0:0%:5,2,0,0 -chr1 45293286 . C . PASS DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:23:19:0:0%:8,11,0,0 0/0:.:9:7:0:0%:3,4,0,0 -chr1 45293287 . C . PASS DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:23:22:0:0%:11,11,0,0 0/0:.:9:9:0:0%:5,4,0,0 -chr1 45293288 . C . PASS DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:25:25:0:0%:14,11,0,0 0/0:.:9:9:0:0%:5,4,0,0 -chr1 45293289 . C . PASS DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:25:21:0:0%:13,8,0,0 0/0:.:9:9:0:0%:5,4,0,0 -chr1 45293290 . G . PASS DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:25:24:0:0%:13,11,0,0 0/0:.:9:7:0:0%:3,4,0,0 -chr1 45293291 . A . PASS DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:25:22:0:0%:11,11,0,0 0/0:.:9:8:0:0%:4,4,0,0 -chr1 45293292 . G . PASS DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:25:24:0:0%:14,10,0,0 0/0:.:9:7:0:0%:4,3,0,0 -chr1 45293293 . G . PASS DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:25:23:0:0%:14,9,0,0 0/0:.:9:7:0:0%:5,2,0,0 -chr1 45293294 . C . PASS DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:25:23:0:0%:12,11,0,0 0/0:.:9:7:0:0%:3,4,0,0 -chr1 45293295 . A . PASS DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:25:23:0:0%:14,9,0,0 0/0:.:9:9:0:0%:5,4,0,0 -chr1 45293296 . C . PASS DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:25:25:0:0%:14,11,0,0 0/0:.:9:9:0:0%:5,4,0,0 -chr1 45293297 . C . PASS DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:25:24:0:0%:13,11,0,0 0/0:.:9:8:0:0%:4,4,0,0 -chr1 45293298 . A . PASS DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:25:24:0:0%:14,10,0,0 0/0:.:9:7:0:0%:5,2,0,0 -chr1 45293299 . C . PASS DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:25:25:0:0%:14,11,0,0 0/0:.:9:9:0:0%:5,4,0,0 -chr1 45293300 . A . PASS DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:25:22:0:0%:14,8,0,0 0/0:.:9:8:0:0%:5,3,0,0 -chr1 45293301 . T . PASS DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:25:24:0:0%:13,11,0,0 0/0:.:9:8:0:0%:5,3,0,0 -chr1 45293302 . C . PASS DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:25:25:0:0%:14,11,0,0 0/0:.:9:9:0:0%:5,4,0,0 -chr1 45293303 . C . PASS DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:25:24:0:0%:13,11,0,0 0/0:.:9:9:0:0%:5,4,0,0 -chr1 45293304 . G . PASS DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:25:24:0:0%:13,11,0,0 0/0:.:9:8:0:0%:4,4,0,0 -chr1 45293305 . T . PASS DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:25:23:0:0%:12,11,0,0 0/0:.:9:9:0:0%:5,4,0,0 -chr1 45293306 . C . PASS DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:25:25:0:0%:14,11,0,0 0/0:.:9:8:0:0%:4,4,0,0 -chr1 45293307 . A . PASS DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:25:24:0:0%:13,11,0,0 0/0:.:9:9:0:0%:5,4,0,0 -chr1 45293308 . G . PASS DP=34;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:25:25:0:0%:14,11,0,0 0/0:.:9:8:0:0%:5,3,0,0 -chr1 45293309 . G . PASS DP=33;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:24:23:0:0%:13,10,0,0 0/0:.:9:9:0:0%:5,4,0,0 -chr1 45293310 . G . PASS DP=32;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:23:22:0:0%:12,10,0,0 0/0:.:9:8:0:0%:5,3,0,0 -chr1 45293484 . T . PASS DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:50:50:0:0%:27,23,0,0 0/0:.:10:8:0:0%:5,3,0,0 -chr1 45293485 . A . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:27,26,0,0 0/0:.:10:9:0:0%:5,4,0,0 -chr1 45293486 . A . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:52:0:0%:26,26,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293487 . G . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:52:0:0%:27,25,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293488 . T . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:52:0:0%:26,26,0,0 0/0:.:10:6:0:0%:5,1,0,0 -chr1 45293489 . C . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:27,26,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293490 . T . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:27,26,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293491 . C . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:52:0:0%:27,25,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293492 . T . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:52:0:0%:27,25,0,0 0/0:.:10:9:0:0%:5,4,0,0 -chr1 45293493 . G . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:27,26,0,0 0/0:.:10:5:0:0%:5,0,0,0 -chr1 45293494 . C . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:27,26,0,0 0/0:.:10:9:0:0%:5,4,0,0 -chr1 45293495 . C . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:27,26,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293496 . C . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:27,26,0,0 0/0:.:10:8:0:0%:5,3,0,0 -chr1 45293497 . T . PASS DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:54:53:0:0%:26,27,0,0 0/0:.:10:7:0:0%:4,3,0,0 -chr1 45293498 . G . PASS DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:54:54:0:0%:27,27,0,0 0/0:.:10:8:0:0%:5,3,0,0 -chr1 45293499 . C . PASS DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:54:54:0:0%:27,27,0,0 0/0:.:10:8:0:0%:4,4,0,0 -chr1 45293500 . T . PASS DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:54:52:0:0%:26,26,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293501 . C . PASS DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:54:51:0:0%:27,24,0,0 0/0:.:10:8:0:0%:5,3,0,0 -chr1 45293502 . T . PASS DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:54:53:0:0%:27,26,0,0 0/0:.:10:8:0:0%:5,3,0,0 -chr1 45293503 . G . PASS DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:54:54:0:0%:27,27,0,0 0/0:.:10:9:0:0%:5,4,0,0 -chr1 45293504 . C . PASS DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:54:53:0:0%:26,27,0,0 0/0:.:10:9:0:0%:5,4,0,0 -chr1 45293505 . C . PASS DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:54:53:0:0%:26,27,0,0 0/0:.:10:9:0:0%:5,4,0,0 -chr1 45293506 . C . PASS DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:54:53:0:0%:27,26,0,0 0/0:.:10:9:0:0%:5,4,0,0 -chr1 45293507 . A . PASS DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:54:54:0:0%:27,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293508 . G . PASS DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:54:54:0:0%:27,27,0,0 0/0:.:10:9:0:0%:5,4,0,0 -chr1 45293509 . T . PASS DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:54:52:0:0%:26,26,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293510 . C . PASS DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:54:52:0:0%:27,25,0,0 0/0:.:10:9:0:0%:5,4,0,0 -chr1 45293511 . T . PASS DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:54:54:0:0%:27,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293512 . T . PASS DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:54:54:0:0%:27,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293513 . A . PASS DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:54:54:0:0%:27,27,0,0 0/0:.:10:9:0:0%:5,4,0,0 -chr1 45293514 . C . PASS DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:54:53:0:0%:27,26,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293515 . C . PASS DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:54:53:0:0%:27,26,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293516 . T . PASS DP=64;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:54:53:0:0%:27,26,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293517 . T . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293518 . A G . PASS DP=63;SOMATIC;SS=2;SSC=34;GPV=1E0;SPV=3.5255E-4 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/1:.:10:6:4:40%:3,3,2,2 -chr1 45293519 . G . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:52:0:0%:26,26,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293520 . C . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/0:.:10:9:0:0%:5,4,0,0 -chr1 45293521 . A . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293522 . T . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293523 . G T . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=8.3871E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:51:1:1.92%:25,26,0,1 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293524 . T . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293525 . G . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293526 . A . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293527 . C . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/0:.:10:9:0:0%:5,4,0,0 -chr1 45293528 . T . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293529 . G . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293530 . G . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293531 . A . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293532 . G . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293533 . C . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293534 . A . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293535 . G . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/0:.:10:9:0:0%:5,4,0,0 -chr1 45293536 . C . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:52:0:0%:25,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293537 . A . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293538 . A . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293539 . C . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293540 . G . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293541 . G . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293542 . G . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:52:0:0%:26,26,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293543 . G . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:52:0:0%:26,26,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293544 . C . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293545 . A . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293546 . A . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293547 . A . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293548 . C . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293549 . T . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293550 . G . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293551 . A . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293552 . T . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:52:0:0%:26,26,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293553 . A . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293554 . G . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:52:0:0%:26,26,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293555 . C . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:52:0:0%:26,26,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293556 . G . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293557 . G . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293558 . G . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293559 . C . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:52:0:0%:25,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293560 . G . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/0:.:10:9:0:0%:4,5,0,0 -chr1 45293561 . A . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293562 . A . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:52:0:0%:25,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293563 . A . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:51:0:0%:25,26,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293564 . T . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:51:0:0%:25,26,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293565 . G . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:52:0:0%:26,26,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293566 . G . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293567 . G . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:51:0:0%:26,25,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293568 . C . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293569 . A . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293570 . A . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293571 . G . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293572 . A . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293573 . T . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293574 . T . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293575 . C . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293576 . C . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293577 . A . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293578 . G . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:51:0:0%:25,26,0,0 0/0:.:10:9:0:0%:4,5,0,0 -chr1 45293579 . C . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:53:0:0%:26,27,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293580 . G . PASS DP=63;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:53:48:0:0%:21,27,0,0 0/0:.:10:9:0:0%:4,5,0,0 -chr1 45293581 . G . PASS DP=62;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:52:52:0:0%:26,26,0,0 0/0:.:10:9:0:0%:4,5,0,0 -chr1 45293582 . G . PASS DP=62;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:52:52:0:0%:26,26,0,0 0/0:.:10:9:0:0%:4,5,0,0 -chr1 45293583 . C . PASS DP=62;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:52:51:0:0%:25,26,0,0 0/0:.:10:9:0:0%:4,5,0,0 -chr1 45293584 . A . PASS DP=62;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:52:50:0:0%:26,24,0,0 0/0:.:10:9:0:0%:4,5,0,0 -chr1 45293585 . C . PASS DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:50:49:0:0%:24,25,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293586 . A . PASS DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:50:50:0:0%:25,25,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293587 . G . PASS DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:50:49:0:0%:24,25,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293588 . G . PASS DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:50:49:0:0%:24,25,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293589 . G . PASS DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:50:50:0:0%:25,25,0,0 0/0:.:10:9:0:0%:4,5,0,0 -chr1 45293590 . C . PASS DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:50:49:0:0%:24,25,0,0 0/0:.:10:5:0:0%:0,5,0,0 -chr1 45293591 . A . PASS DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:50:50:0:0%:25,25,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293592 . G . PASS DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:50:50:0:0%:25,25,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293593 . G . PASS DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:50:50:0:0%:25,25,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293594 . G . PASS DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:50:49:0:0%:24,25,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293595 . A . PASS DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:50:49:0:0%:25,24,0,0 0/0:.:10:9:0:0%:4,5,0,0 -chr1 45293596 . C . PASS DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:50:49:0:0%:24,25,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293597 . T . PASS DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:50:49:0:0%:24,25,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293598 . T . PASS DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:50:48:0:0%:23,25,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293599 . G . PASS DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:50:49:0:0%:25,24,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293600 . C . PASS DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:50:49:0:0%:24,25,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293601 . A . PASS DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:50:49:0:0%:24,25,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293602 . G . PASS DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:50:50:0:0%:25,25,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293603 . G . PASS DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:50:49:0:0%:24,25,0,0 0/0:.:10:9:0:0%:4,5,0,0 -chr1 45293604 . C . PASS DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:50:49:0:0%:24,25,0,0 0/0:.:10:5:0:0%:0,5,0,0 -chr1 45293605 . T . PASS DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:50:50:0:0%:25,25,0,0 0/0:.:10:9:0:0%:4,5,0,0 -chr1 45293606 . G . PASS DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:50:49:0:0%:24,25,0,0 0/0:.:10:8:0:0%:3,5,0,0 -chr1 45293607 . C . PASS DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:50:49:0:0%:24,25,0,0 0/0:.:10:5:0:0%:0,5,0,0 -chr1 45293608 . C . PASS DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:50:50:0:0%:25,25,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293609 . T . PASS DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:50:49:0:0%:24,25,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293610 . T . PASS DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:50:50:0:0%:25,25,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293611 . C . PASS DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:50:49:0:0%:24,25,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293612 . T . PASS DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:50:50:0:0%:25,25,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293613 . G . PASS DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:50:50:0:0%:25,25,0,0 0/0:.:10:8:0:0%:3,5,0,0 -chr1 45293614 . C . PASS DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:50:49:0:0%:24,25,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293615 . C . PASS DP=60;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:50:49:0:0%:24,25,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293616 . T . PASS DP=57;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:47:47:0:0%:22,25,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr1 45293617 . T . PASS DP=57;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:47:46:0:0%:21,25,0,0 0/0:.:10:5:0:0%:0,5,0,0 -chr1 45293618 . G . PASS DP=57;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:47:46:0:0%:21,25,0,0 0/0:.:10:5:0:0%:0,5,0,0 -chr1 45293619 . T . PASS DP=57;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:47:46:0:0%:21,25,0,0 0/0:.:10:9:0:0%:4,5,0,0 -chr1 45293620 . C . PASS DP=57;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:47:47:0:0%:22,25,0,0 0/0:.:10:9:0:0%:4,5,0,0 -chr1 45293621 . T . PASS DP=57;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:47:47:0:0%:22,25,0,0 0/0:.:10:6:0:0%:1,5,0,0 -chr1 45293622 . C . PASS DP=57;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:47:47:0:0%:22,25,0,0 0/0:.:10:10:0:0%:5,5,0,0 -chr5 156750993 . T . PASS DP=30;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:22:22:0:0%:10,12,0,0 0/0:.:8:7:0:0%:3,4,0,0 -chr5 156750994 . G . PASS DP=30;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:22:22:0:0%:10,12,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156750995 . A . PASS DP=30;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:22:22:0:0%:10,12,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156750996 . G . PASS DP=27;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:19:19:0:0%:10,9,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156750997 . G . PASS DP=27;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:19:19:0:0%:10,9,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156750998 . A . PASS DP=27;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:19:19:0:0%:10,9,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156750999 . G . PASS DP=27;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:19:19:0:0%:10,9,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751000 . C . PASS DP=27;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:19:19:0:0%:10,9,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751001 . A . PASS DP=27;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:19:19:0:0%:10,9,0,0 0/0:.:8:7:0:0%:4,3,0,0 -chr5 156751006 . G . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751007 . G . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751008 . A . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751009 . T . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751010 . G . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751011 . G . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751012 . A . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:19:0:0%:9,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751013 . C . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:7:0:0%:4,3,0,0 -chr5 156751014 . C . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751015 . C . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751016 . A . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751017 . T . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751018 . T . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:7:0:0%:4,3,0,0 -chr5 156751019 . G . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751020 . T . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:7:0:0%:4,3,0,0 -chr5 156751021 . C . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:7:0:0%:4,3,0,0 -chr5 156751022 . C . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751023 . T . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751024 . C . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:19:0:0%:10,9,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751025 . G . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:19:0:0%:9,10,0,0 0/0:.:8:7:0:0%:3,4,0,0 -chr5 156751026 . C . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:7:0:0%:3,4,0,0 -chr5 156751027 . C . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751028 . A . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751029 . T . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:19:0:0%:10,9,0,0 0/0:.:8:7:0:0%:4,3,0,0 -chr5 156751030 . A . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:19:0:0%:9,10,0,0 0/0:.:8:7:0:0%:4,3,0,0 -chr5 156751031 . G . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751032 . A . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:19:0:0%:9,10,0,0 0/0:.:8:7:0:0%:4,3,0,0 -chr5 156751033 . G . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:7:0:0%:4,3,0,0 -chr5 156751034 . G . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:7:0:0%:4,3,0,0 -chr5 156751035 . A . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:7:0:0%:4,3,0,0 -chr5 156751036 . C . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751037 . T . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751038 . T . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:7:0:0%:4,3,0,0 -chr5 156751039 . T . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751040 . C . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751041 . A . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751042 . C . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751043 . A . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751044 . A . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751045 . A . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:19:0:0%:10,9,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751046 . C . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751047 . A . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:7:0:0%:4,3,0,0 -chr5 156751048 . G . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:19:0:0%:9,10,0,0 0/0:.:8:6:0:0%:2,4,0,0 -chr5 156751049 . T . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751050 . C . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751051 . C . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751052 . T . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751053 . T . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751054 . C . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751055 . T . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751056 . T . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751057 . C . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751058 . T . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:19:0:0%:10,9,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751059 . T . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751060 . C . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751061 . A . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:19:0:0%:9,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751062 . C . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751063 . A . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:6:0:0%:4,2,0,0 -chr5 156751064 . C . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751065 . A . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:18:0:0%:8,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751066 . T . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751067 . C . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:7:0:0%:4,3,0,0 -chr5 156751068 . T . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:7:0:0%:4,3,0,0 -chr5 156751069 . G . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751070 . C . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751071 . T . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751072 . C . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751073 . A . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:10,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751074 . A . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:19:0:0%:9,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751075 . C . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:18:0:0%:8,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156751076 . A . PASS DP=28;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:18:0:0%:8,10,0,0 0/0:.:8:5:0:0%:2,3,0,0 -chr5 156751077 . T . PASS DP=26;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:18:17:0:0%:7,10,0,0 0/0:.:8:6:0:0%:2,4,0,0 -chr5 156751078 . C . PASS DP=24;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:16:15:0:0%:5,10,0,0 0/0:.:8:8:0:0%:4,4,0,0 -chr5 156788529 . C . PASS DP=20;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:11:9:0:0%:4,5,0,0 0/0:.:9:7:0:0%:3,4,0,0 -chr5 156788530 . T . PASS DP=21;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:12:12:0:0%:6,6,0,0 0/0:.:9:6:0:0%:2,4,0,0 -chr5 156788531 . C CA . PASS DP=21;SS=1;SSC=9;GPV=1.9541E-4;SPV=1.1491E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/1:.:11:7:4:36.36%:4,3,2,2 1/1:.:10:2:6:75%:1,1,3,3 -chr5 156788532 . A . PASS DP=22;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:12:8:0:0%:5,3,0,0 0/0:.:10:4:0:0%:3,1,0,0 -chr5 156788533 . A . PASS DP=22;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:12:8:0:0%:5,3,0,0 0/0:.:10:4:0:0%:3,1,0,0 -chr5 156788534 . A . PASS DP=22;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:12:7:0:0%:5,2,0,0 0/0:.:10:3:0:0%:3,0,0,0 -chr5 156788535 . A . PASS DP=22;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:12:8:0:0%:5,3,0,0 0/0:.:10:4:0:0%:3,1,0,0 -chr5 156788536 . C . PASS DP=22;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:12:12:0:0%:7,5,0,0 0/0:.:10:9:0:0%:5,4,0,0 -chr5 156788537 . A . PASS DP=22;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:12:12:0:0%:7,5,0,0 0/0:.:10:8:0:0%:4,4,0,0 -chr5 156788538 . G . PASS DP=22;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:12:12:0:0%:7,5,0,0 0/0:.:10:10:0:0%:6,4,0,0 -chr5 156788539 . A . PASS DP=22;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:12:11:0:0%:7,4,0,0 0/0:.:10:10:0:0%:6,4,0,0 -chr5 156788540 . C . PASS DP=22;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:12:10:0:0%:5,5,0,0 0/0:.:10:10:0:0%:6,4,0,0 -chr5 156788541 . G . PASS DP=22;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:12:11:0:0%:6,5,0,0 0/0:.:10:10:0:0%:6,4,0,0 -chr5 156788542 . T . PASS DP=21;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:11:10:0:0%:5,5,0,0 0/0:.:10:9:0:0%:5,4,0,0 -chr5 156788543 . G . PASS DP=20;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:10:10:0:0%:6,4,0,0 0/0:.:10:10:0:0%:6,4,0,0 -chr5 156788544 . T . PASS DP=20;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:10:9:0:0%:5,4,0,0 0/0:.:10:10:0:0%:6,4,0,0 -chr5 156788545 . T . PASS DP=20;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:10:10:0:0%:6,4,0,0 0/0:.:10:10:0:0%:6,4,0,0 -chr5 156788546 . C . PASS DP=20;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:10:10:0:0%:6,4,0,0 0/0:.:10:10:0:0%:6,4,0,0 -chr5 156788547 . C . PASS DP=19;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:10:9:0:0%:5,4,0,0 0/0:.:9:8:0:0%:4,4,0,0 -chr5 156788548 . A . PASS DP=19;SS=0;SSC=0;GPV=1E0;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:10:9:0:0%:5,4,0,0 0/0:.:9:9:0:0%:5,4,0,0
--- a/varscan/tool_dependencies.xml Fri Mar 07 06:17:32 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,19 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="VarScan" version="2.3.5"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://downloads.sourceforge.net/project/varscan/VarScan.v2.3.5.jar</action> - <action type="move_file"> - <source>VarScan.v2.3.5.jar</source> - <destination>$INSTALL_DIR/jars</destination> - </action> - <action type="set_environment"> - <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/jars</environment_variable> - </action> - </actions> - </install> - <readme> - </readme> - </package> -</tool_dependency>
--- a/varscan/varscan_mpileup.pl Fri Mar 07 06:17:32 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,121 +0,0 @@ -#!/usr/bin/perl - -use strict; -use Cwd; - -die qq( -Bad numbr of inputs - -) if(!@ARGV); - -my $options =""; -my $file=""; -my $command=""; -my $output=""; -my $working_dir = cwd(); -my $temp_vcf = "$working_dir/temp"; -my $log=""; - -foreach my $input (@ARGV) -{ - my @tmp = split "::", $input; - if($tmp[0] eq "COMMAND") - { - $command = $tmp[1]; - } - elsif($tmp[0] eq "INPUT") - { - $file = $tmp[1]; - } - elsif($tmp[0] eq "OPTION") - { - my @p = split(/\s+/,$tmp[1]); - if ($p[0] =~ m/variants|strand-filter|output-vcf/ && $p[1] == 0) { - next; - } - - $options = "$options ${tmp[1]}"; - } - elsif($tmp[0] eq "OUTPUT") - { - $output = $tmp[1]; - } - elsif($tmp[0] eq "LOG") - { - $log = $tmp[1]; - } - else - { - die("Unknown Input: $input\n"); - } -} - -system ("$command $file $options 1>$temp_vcf 2>$log"); - -vs2vcf($temp_vcf, $output); - - -sub vs2vcf -{ - - # - # G l o b a l v a r i a b l e s - # - my $version = '0.1'; - - # - # Read in file - # - my $input = shift; - my $output = shift; - my $chr_ord = shift; - open(IN, $input) or die "Can't open $input': $!\n"; - open(OUT, ">$output") or die "Can't create $output': $!\n"; - my %output; - - while ( <IN> ) - { - if ( /^#/ ) - { - print OUT; - next; - } - chomp; - my $line = $_; - - my @flds = split ( "\t", $line ); - my $ref = $flds[3]; - my $alt = $flds[4]; - # - # Deletion of bases - # - if ( $alt =~ /^\-/ ) - { - ($flds[3], $flds[4]) = ($ref.substr($alt,1), $ref); - } - - # - # Insertion of bases - # - if ( $alt =~ /^\+/ ) - { - $flds[4] = $ref.substr($alt,1); - } - print OUT join( "\t", @flds),"\n" unless defined $chr_ord; - $output{$flds[0]}{$flds[1]} = join( "\t", @flds)."\n" if defined $chr_ord; - } - close(IN); - # if chromosome order given return in sorted order - if(defined $chr_ord) - { - for my $chrom (@{ $chr_ord }) - { - for my $pos (sort {$a<=>$b} keys %{ $output{$chrom} }) - { - print OUT $output{$chrom}{$pos}; - } - } - } - close(OUT); -} -
--- a/varscan/varscan_mpileup.xml Fri Mar 07 06:17:32 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,124 +0,0 @@ -<tool id="varscan_mpileup" name="VarScan mpileup" version="2.3.5"> - <description> - mutation caller for targeted, exome, and whole-genome resequencing - </description> - <requirements> - <requirement type="package" version="2.3.5">VarScan</requirement> - </requirements> - <command interpreter="perl"> - - varscan_mpileup.pl - "COMMAND::java -jar \$JAVA_JAR_PATH/VarScan.v2.3.5.jar $exe_command" - "INPUT::$in_file" - "OUTPUT::$output" - "LOG::$log" - "OPTION::--min-coverage $min_coverage" - "OPTION::--min-reads2 $min_reads2" - "OPTION::--min-avg-qual $min_avg_qual" - "OPTION::--min-var-freq $min_var_freq" - "OPTION::--min-freq-for-hom $min_freq_for_hom" - "OPTION::--p-value $p_value" - "OPTION::--strand-filter $strand_filter" - "OPTION::--output-vcf 1" - - #if ($vcf_sample_list): - "OPTION::--vcf-sample-list $vcf_sample_list" - #end if - "OPTION::--variants $variants" - - - - </command> - - <inputs> - - <param name="exe_command" type="select" label="Command" help="" optional="false"> - <option value="mpileup2snp" >mpileup2snp</option> - <option value="mpileup2indel">mpileup2indel</option> - <option value="mpileup2cns">mpileup2cns</option> - </param> - <param name="in_file" type="data" format="pileup" label="mpileup file" help="The SAMtools mpileup file" /> - <param name="min_coverage" type="integer" label="min-coverage" help="" optional="true" value="8"/> - <param name="min_reads2" type="integer" label="min-reads2" help="" optional="true" value="2"/> - <param name="min_avg_qual" type="integer" label="min-avg-qual" help="" optional="true" value="15"/> - <param name="min_var_freq" type="float" label="min-var-freq" help="" optional="true" value="0.01"/> - <param name="min_freq_for_hom" type="float" label="min-freq-for-hom" help="" optional="true" value="0.75"/> - <param name="p_value" type="text" label="p-value" help="" optional="true" value="0.99"/> - <param name="strand_filter" type="integer" label="strand-filter" help="" optional="true" value="1"/> - <param name="vcf_sample_list" type="data" label="vcf-sample-list" format="txt" help="" optional="true" /> - <param name="variants" type="integer" label="variants" help="Set to 1 to report only variants" optional="true" value="1"/> - - - </inputs> - <outputs> - <data type="data" format="vcf" name="output" label="${tool.name} result on ${on_string}"/> - <data type="data" format="txt" name="log" label="${tool.name} result on ${on_string} (log) "/> - </outputs> - - <help> - -.. class:: infomark - -**What it does** - -:: - - VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments. The newest version, VarScan 2, is written in Java, so it runs on most operating systems. It can be used to detect different types of variation: - - Germline variants (SNPs an dindels) in individual samples or pools of samples. - Multi-sample variants (shared or private) in multi-sample datasets (with mpileup). - Somatic mutations, LOH events, and germline variants in tumor-normal pairs. - Somatic copy number alterations (CNAs) in tumor-normal exome data. - - -**Input** - -:: - - mpileup file - The SAMtools mpileup file - - -**Parameters** - -:: - - commands - mpileup2snp Identify SNPs from an mpileup file - mpileup2indel Identify indels an mpileup file - mpileup2cns Call consensus and variants from an mpileup file - - min-coverage - Minimum read depth at a position to make a call [8] - - min-reads2 - Minimum supporting reads at a position to call variants [2] - - min-avg-qual - Minimum base quality at a position to count a read [15] - - min-var-freq - Minimum variant allele frequency threshold [0.01] - - min-freq-for-hom - Minimum frequency to call homozygote [0.75] - - p-value - Default p-value threshold for calling variants [99e-02] - - strand-filter - Ignore variants with >90% support on one strand [1] - - output-vcf - If set to 1, outputs in VCF format - - vcf-sample-list - For VCF output, a list of sample names in order, one per line - - variants - Report only variant (SNP/indel) positions [0] - - - - </help> -</tool> -
--- a/varscan/varscan_processSomatic.pl Fri Mar 07 06:17:32 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,223 +0,0 @@ -#!/usr/bin/perl - - -use strict; -use Cwd; - -die qq( -Bad numbr of inputs - -) if(!@ARGV); - -my $options =""; -my $command=""; -my $input=""; -#my $output=""; -my $working_dir = cwd(); -my $log = ''; -my %outfiles; -foreach my $arg (@ARGV) -{ - my @tmp = split "::", $arg; - if($tmp[0] eq "COMMAND") - { - $command = $tmp[1]; - } - elsif($tmp[0] eq "INPUT") - { - $input = $tmp[1]; - } - elsif($tmp[0] eq "OPTION") - { - my @p = split(/\s+/,$tmp[1]); - $options = "$options ${tmp[1]}"; - } - elsif($tmp[0] eq "OUTPUT") - { - my @p = split(/\s+/,$tmp[1]); - $p[0] = substr($p[0],2); - $outfiles{$p[0]} = $p[1]; - } - - elsif($tmp[0] eq "LOG") - { - $log = $tmp[1]; - } - else - { - die("Unknown Input: $input\n"); - } -} -system("ln -s $input $working_dir/in.dat"); - - - -## RUN -$command = "$command $working_dir/in.dat $options > $log 2>&1"; -system($command); - -## if tabular files are kept, write them to galaxy-datafile -if ($outfiles{'loh'} ne 'None') { - ## - system("cp '$working_dir/in.dat.LOH' '".$outfiles{'loh'}."'"); - system("cp '$working_dir/in.dat.LOH.hc' '".$outfiles{'loh'}."'"); - system("cp '$working_dir/in.dat.Germline' '".$outfiles{'germ'}."'"); - system("cp '$working_dir/in.dat.Germline.hc' '".$outfiles{'germ_hc'}."'"); - system("cp '$working_dir/in.dat.Somatic' '".$outfiles{'som'}."'"); - system("cp '$working_dir/in.dat.Somatic.hc' '".$outfiles{'som_hc'}."'"); -} -## if vcf files are kept, generate them, and write to galaxy-datafile -if ($outfiles{'loh_hc_vcf'} ne 'None') { - tab2vcf($working_dir,'in.dat.LOH.hc',$outfiles{'loh_hc_vcf'}); - tab2vcf($working_dir,'in.dat.Germline.hc',$outfiles{'germ_hc_vcf'}); - tab2vcf($working_dir,'in.dat.Somatic.hc',$outfiles{'som_hc_vcf'}); -} -exit; - -sub tab2vcf -{ - my $wd = shift; - my $in = shift; - my $out = shift; - open OUT, ">$out"; - print OUT "##fileformat=VCFv4.1\n"; - print OUT "##source=processSomatic\n"; - print OUT '##INFO=<ID=DP,Number=1,Type=Integer,Description="Total depth of quality bases">'."\n"; - print OUT '##INFO=<ID=SS,Number=1,Type=String,Description="Somatic status of variant (Germline,Somatic,LOH)">'."\n"; - print OUT '##INFO=<ID=VPV,Number=1,Type=Float,Description="Variant P-value">'."\n"; - print OUT '##INFO=<ID=SPV,Number=1,Type=Float,Description="Somatic Variant P-value">'."\n"; - print OUT '##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">'."\n"; - print OUT '##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">'."\n"; - print OUT '##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">'."\n"; - print OUT '##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)">'."\n"; - print OUT '##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)">'."\n"; - print OUT '##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency">'."\n"; - print OUT '##FORMAT=<ID=DP4,Number=1,Type=String,Description="Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev">'."\n"; - print OUT '#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR'."\n"; - open IN, "$wd/$in"; - my $head = <IN>; - while (<IN>) { - chomp; - my @p = split(/\t/,$_); - my $td = $p[4] + $p[5] + $p[8] + $p[9]; - my $vpv = sprintf('%.3E',$p[13]); - my $spv = sprintf('%.3E',$p[14]); - my $info = "DP=$td;SS=$p[12];VPV=$vpv;SPV=$spv"; - ## gt normal string - my $gtnormal = ''; - if ("$p[7]" eq "$p[2]") { - $gtnormal = "0/0"; - } - elsif ("$p[7]" eq "$p[3]") { - $gtnormal = "1/1"; - } - else { - $gtnormal = "0/1"; - } - my $nsum = $p[4] + $p[5]; - $gtnormal .= ":.:$nsum:$p[4]:$p[5]:$p[6]:$p[19],$p[20],$p[21],$p[22]"; - ## gt tumor string - my $gttumor = ''; - if ("$p[11]" eq "$p[2]") { - $gttumor = "0/0"; - } - elsif ("$p[11]" eq "$p[3]") { - $gttumor = "1/1"; - } - else { - $gttumor = "0/1"; - } - my $tsum = $p[8] + $p[9]; - $gttumor .= ":.:$tsum:$p[8]:$p[9]:$p[10]:$p[15],$p[16],$p[17],$p[18]"; - - ## outline - my $line = "$p[0]\t$p[1]\t.\t$p[2]\t$p[3]\t.\tPASS\t$info\tGT:GQ:DP:RD:AD:FREQ:DP4\t$gtnormal\t$gttumor\n"; - print OUT $line; - } - close IN; - close OUT; -} -sub vs2vcf -{ - - # - # G l o b a l v a r i a b l e s - # - my $version = '0.1'; - - # - # Read in file - # - my $input = shift; - my $output = shift; - my $chr_ord = shift; - open(IN, $input) or die "Can't open $input': $!\n"; - open(OUT, ">$output") or die "Can't create $output': $!\n"; - my %output; - - while ( <IN> ) - { - if ( /^#/ ) - { - print OUT; - next; - } - chomp; - my $line = $_; - - my @flds = split ( "\t", $line ); - my $ref = $flds[3]; - my $alt = $flds[4]; - # - # Deletion of bases - # - if ( $alt =~ /^\-/ ) - { - ($flds[3], $flds[4]) = ($ref.substr($alt,1), $ref); - } - - # - # Insertion of bases - # - if ( $alt =~ /^\+/ ) - { - $flds[4] = $ref.substr($alt,1); - } - ## insert dot for reference positions. - if ($flds[4] eq '') { - $flds[4] = '.'; - } - print OUT join( "\t", @flds),"\n" unless defined $chr_ord; - $output{$flds[0]}{$flds[1]} = join( "\t", @flds)."\n" if defined $chr_ord; - } - close(IN); - # if chromosome order given return in sorted order - if(defined $chr_ord) - { - for my $chrom (@{ $chr_ord }) - { - for my $pos (sort {$a<=>$b} keys %{ $output{$chrom} }) - { - print OUT $output{$chrom}{$pos}; - } - } - } - close(OUT); -} - - -sub chromosome_order -{ - my $input = shift; - # calculate flagstats - my $COMM = "samtools view -H $input | grep '^\@SQ'"; - my @SQ = `$COMM`; - chomp @SQ; - for(my $i = 0; $i <= $#SQ; $i++) - { - $SQ[$i] =~ s/^\@SQ\tSN:(.*?)\tLN:\d+$/$1/; - } - return(@SQ); -} - -
--- a/varscan/varscan_processSomatic.xml Fri Mar 07 06:17:32 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,154 +0,0 @@ -<tool id="varscan_processSomatic" name="ProcessSomatic" version="2.3.5"> - <description> - Extract HC calls from Somatic Caller - </description> - <requirements> - <requirement type="package" version="2.3.5">VarScan</requirement> - </requirements> - <command interpreter="perl"> - - varscan_processSomatic.pl - "COMMAND::java -jar \$JAVA_JAR_PATH/VarScan.v2.3.5.jar processSomatic" - "INPUT::$input" - "LOG::$log" - - "OPTION::--min-tumor-freq $min_tumor_freq" - "OPTION::--max-normal-freq $max_normal_freq" - "OPTION::--p-value $p_value" - "OUTPUT::--loh $loh" - "OUTPUT::--loh_hc $loh_hc" - "OUTPUT::--germ $germ" - "OUTPUT::--germ_hc $germ_hc" - "OUTPUT::--som $som" - "OUTPUT::--som_hc $som_hc" - "OUTPUT::--som_hc_vcf $som_hc_vcf" - "OUTPUT::--germ_hc_vcf $germ_hc_vcf" - "OUTPUT::--loh_hc_vcf $loh_hc_vcf" - - </command> - - <inputs> - - <param name="input" type="data" format="txt" label="Input File" help="VarScan Somatics output file in native format" /> - - <param name="min_tumor_freq" type="float" label="min-tumor-freq" help="Minimum variant allele frequency in tumor" optional="true" value="0.10"/> - <param name="max_normal_freq" type="float" label="max-normal-freq" help="Maximum variant allele frequency in normal" optional="true" value="0.05"/> - <param name="p_value" type="text" label="p-value" help="P-value for high-confidence calling" optional="true" value="0.07"/> - <param name="outtype" type="select" label="Output Type:" default="1"> - <option value="0">Native VarScan Tables</option> - <option value="1">VCF format (only High Confidence)</option> - <option value="2">Both</option> - </param> - - </inputs> - <outputs> - <data type="data" format="txt" name="log" label="${tool.name} result on ${on_string} (log) " /> - <data type="data" format="txt" name="loh" label="${tool.name} result on ${on_string} (loh) " > - <filter>outtype != "1"</filter> - </data> - <data type="data" format="txt" name="loh_hc" label="${tool.name} result on ${on_string} (loh_hc)"> - <filter>outtype != "1"</filter> - </data> - - <data type="data" format="txt" name="germ" label="${tool.name} result on ${on_string} (germline)" > - <filter>outtype != "1"</filter> - </data> - - <data type="data" format="txt" name="germ_hc" label="${tool.name} result on ${on_string} (germline_hc)"> - <filter>outtype != "1"</filter> - </data> - - <data type="data" format="txt" name="som" label="${tool.name} result on ${on_string} (somatic)" > - <filter>outtype != "1"</filter> - </data> - - <data type="data" format="txt" name="som_hc" label="${tool.name} result on ${on_string} (somatic_hc)" > - <filter>outtype != "1"</filter> - </data> - - <data type="data" format="vcf" name="som_hc_vcf" label="${tool.name} result on ${on_string} (Somatic_HC.vcf)" > - <filter>outtype != "0"</filter> - </data> - - <data type="data" format="vcf" name="loh_hc_vcf" label="${tool.name} result on ${on_string} (LOH_HC.vcf)" > - <filter>outtype != "0"</filter> - </data> - - <data type="data" format="vcf" name="germ_hc_vcf" label="${tool.name} result on ${on_string} (Germline_HC.vcf)" > - <filter>outtype != "0"</filter> - </data> - - - - - </outputs> - - <help> - -.. class:: infomark - -**What it does** - -:: - - VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments. The newest version, VarScan 2, is written in Java, so it runs on most operating systems. It can be used to detect different types of variation: - - Germline variants (SNPs an dindels) in individual samples or pools of samples. - Multi-sample variants (shared or private) in multi-sample datasets (with mpileup). - Somatic mutations, LOH events, and germline variants in tumor-normal pairs. - Somatic copy number alterations (CNAs) in tumor-normal exome data. - - -**Input** - -:: - - mpileup normal file - The SAMtools mpileup file for normal - mpileup tumor file - The SAMtools mpileup file for tumor - - -**Parameters** - -:: - - min-coverage - Minimum read depth at a position to make a call [8] - - min-coverage-normal - Minimum coverage in normal to call somatic [8] - - min-coverage-tumor - Minimum coverage in tumor to call somatic [6] - - min-var-freq - Minimum variant frequency to call a heterozygote [0.10] - - min-freq-for-hom - Minimum frequency to call homozygote [0.75] - - normal-purity - Estimated purity (non-tumor content) of normal sample [1.00] - - tumor-purity - Estimated purity (tumor content) of tumor sample [1.00] - - p-value - Default p-value threshold for calling variants [0.99] - - somatic-p-value - P-value threshold to call a somatic site [0.05] - - strand-filter - If set to 1, removes variants with >90% strand bias - - validation - If set to 1, outputs all compared positions even if non-variant - - output-vcf - If set to 1, outputs in VCF format [Default] - - - - </help> -</tool> -
--- a/varscan/varscan_somatic.native.xml Fri Mar 07 06:17:32 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,139 +0,0 @@ -<tool id="varscan_somatic" name="VarScan Somatic (Native Output)" version="2.3.5"> - <description> - somatic mutation caller for cancer genomics - </description> - <requirements> - <requirement type="package" version="2.3.5">VarScan</requirement> - </requirements> - <command interpreter="perl"> - - varscan_somatic.pl - "COMMAND::java -jar \$JAVA_JAR_PATH/VarScan.v2.3.5.jar somatic" - "NORMAL::$normal" - "TUMOR::$tumor" - "TUMORBAM::$tumorbam" - "SNP::$snp" - "INDEL::$indel" - "LOG::$log" - - "OPTION::--min-coverage $min_coverage" - "OPTION::--min-coverage-normal $min_coverage_normal" - "OPTION::--min-coverage-tumor $min_coverage_tumor" - - "OPTION::--min-var-freq $min_var_freq" - "OPTION::--min-freq-for-hom $min_freq_for_hom" - - "OPTION::--normal-purity $normal_purity" - "OPTION::--tumor-purity $tumor_purity" - - "OPTION::--p-value $p_value" - "OPTION::--somatic-p-value $somatic_p_value" - - "OPTION::--strand-filter $strand_filter" - "OPTION::--validation $validation" - - - - </command> - - <inputs> - - <param name="normal" type="data" format="pileup" label="normal mpileup file" help="The SAMtools mpileup file for normal sample" /> - <param name="tumor" type="data" format="pileup" label="tumor mpileup file" help="The SAMtools mpileup file for tumor sample" /> - <param name="tumorbam" type="data" format="bam" label="tumor BAM file" help="The BAM file of the tumor sample used in mpileup step" /> - - <param name="min_coverage" type="integer" label="min-coverage" help="" optional="true" value="8"/> - <param name="min_coverage_normal" type="integer" label="min-coverage-normal" help="" optional="true" value="8"/> - <param name="min_coverage_tumor" type="integer" label="min-coverage-tumor" help="" optional="true" value="6"/> - - <param name="min_var_freq" type="float" label="min-var-freq" help="" optional="true" value="0.10"/> - <param name="min_freq_for_hom" type="float" label="min-freq-for-hom" help="" optional="true" value="0.75"/> - - <param name="normal_purity" type="float" label="normal-purity" help="" optional="true" value="1.00"/> - <param name="tumor_purity" type="float" label="tumor-purity" help="" optional="true" value="1.00"/> - - - <param name="p_value" type="text" label="p-value" help="" optional="true" value="0.99"/> - <param name="somatic_p_value" type="text" label="somatic-p-value" help="" optional="true" value="0.05"/> - - <param name="strand_filter" type="integer" label="strand-filter" help="" optional="true" value="1"/> - <param name="validation" type="integer" label="validation" help="" optional="true" value="0"/> - - </inputs> - <outputs> - <data type="data" format="txt" name="log" label="${tool.name} result on ${on_string} (log) "/> - <data type="data" format="txt" name="snp" label="${tool.name} result on ${on_string} (SNP)" /> - <data type="data" format="txt" name="indel" label="${tool.name} result on ${on_string} (INDEL)" /> - - - </outputs> - - <help> - -.. class:: infomark - -**What it does** - -:: - - VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments. The newest version, VarScan 2, is written in Java, so it runs on most operating systems. It can be used to detect different types of variation: - - Germline variants (SNPs an dindels) in individual samples or pools of samples. - Multi-sample variants (shared or private) in multi-sample datasets (with mpileup). - Somatic mutations, LOH events, and germline variants in tumor-normal pairs. - Somatic copy number alterations (CNAs) in tumor-normal exome data. - - -**Input** - -:: - - mpileup normal file - The SAMtools mpileup file for normal - mpileup tumor file - The SAMtools mpileup file for tumor - - -**Parameters** - -:: - - min-coverage - Minimum read depth at a position to make a call [8] - - min-coverage-normal - Minimum coverage in normal to call somatic [8] - - min-coverage-tumor - Minimum coverage in tumor to call somatic [6] - - min-var-freq - Minimum variant frequency to call a heterozygote [0.10] - - min-freq-for-hom - Minimum frequency to call homozygote [0.75] - - normal-purity - Estimated purity (non-tumor content) of normal sample [1.00] - - tumor-purity - Estimated purity (tumor content) of tumor sample [1.00] - - p-value - Default p-value threshold for calling variants [0.99] - - somatic-p-value - P-value threshold to call a somatic site [0.05] - - strand-filter - If set to 1, removes variants with >90% strand bias - - validation - If set to 1, outputs all compared positions even if non-variant - - output-vcf - If set to 1, outputs in VCF format [Default] - - - - </help> -</tool> -
--- a/varscan/varscan_somatic.pl Fri Mar 07 06:17:32 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,173 +0,0 @@ -#!/usr/bin/perl - - -use strict; -use Cwd; - -die qq( -Bad numbr of inputs - -) if(!@ARGV); - -my $options =""; -my $normal=""; -my $command=""; -my $tumor=""; -my $tumorbam = ""; -my $output=""; -my $snp=""; -my $indel=""; -my $working_dir = cwd(); -my $log = ''; - -foreach my $input (@ARGV) -{ - my @tmp = split "::", $input; - if($tmp[0] eq "COMMAND") - { - $command = $tmp[1]; - } - elsif($tmp[0] eq "NORMAL") - { - $normal = $tmp[1]; - } - elsif($tmp[0] eq "TUMOR") - { - $tumor = $tmp[1]; - } - elsif($tmp[0] eq "TUMORBAM") - { - $tumorbam = $tmp[1]; - } - elsif($tmp[0] eq "OPTION") - { - my @p = split(/\s+/,$tmp[1]); - if ($p[0] =~ m/validation|strand-filter|output-vcf/ && $p[1] == 0) { - next; - } - $options = "$options ${tmp[1]}"; - } - elsif($tmp[0] eq "OUTPUT") - { - $output = $tmp[1]; - } - elsif($tmp[0] eq "SNP") - { - $snp = $tmp[1]; - } - elsif($tmp[0] eq "INDEL") - { - $indel = $tmp[1]; - } - - elsif($tmp[0] eq "LOG") - { - $log = $tmp[1]; - } - - else - { - die("Unknown Input: $input\n"); - } -} - -## VCF OUTPUT -if ($output ne '') { - system ("$command $normal $tumor $options --output-snp $working_dir/out.snp --output-indel $working_dir/out.indel 2>$log"); - my $indels = "$working_dir/out.indel.vcf"; - my $snps = "$working_dir/out.snp.vcf"; - - system("grep -v '^\#' $indels | grep -v '^chrom position' >> $snps"); - my @chr_ord = chromosome_order($tumorbam); - - vs2vcf($snps, $output,\@chr_ord); -} -## SNP/INDEL OUTPUT -else { - system ("$command $normal $tumor $options --output-snp $snp --output-indel $indel 2>$log"); -} - -sub vs2vcf -{ - - # - # G l o b a l v a r i a b l e s - # - my $version = '0.1'; - - # - # Read in file - # - my $input = shift; - my $output = shift; - my $chr_ord = shift; - open(IN, $input) or die "Can't open $input': $!\n"; - open(OUT, ">$output") or die "Can't create $output': $!\n"; - my %output; - - while ( <IN> ) - { - if ( /^#/ ) - { - print OUT; - next; - } - chomp; - my $line = $_; - - my @flds = split ( "\t", $line ); - my $ref = $flds[3]; - my $alt = $flds[4]; - # - # Deletion of bases - # - if ( $alt =~ /^\-/ ) - { - ($flds[3], $flds[4]) = ($ref.substr($alt,1), $ref); - } - - # - # Insertion of bases - # - if ( $alt =~ /^\+/ ) - { - $flds[4] = $ref.substr($alt,1); - } - ## insert dot for reference positions. - if ($flds[4] eq '') { - $flds[4] = '.'; - } - print OUT join( "\t", @flds),"\n" unless defined $chr_ord; - $output{$flds[0]}{$flds[1]} = join( "\t", @flds)."\n" if defined $chr_ord; - } - close(IN); - # if chromosome order given return in sorted order - if(defined $chr_ord) - { - for my $chrom (@{ $chr_ord }) - { - for my $pos (sort {$a<=>$b} keys %{ $output{$chrom} }) - { - print OUT $output{$chrom}{$pos}; - } - } - } - close(OUT); -} - - -sub chromosome_order -{ - my $input = shift; - # calculate flagstats - my $COMM = "samtools view -H $input | grep '^\@SQ'"; - my @SQ = `$COMM`; - chomp @SQ; - for(my $i = 0; $i <= $#SQ; $i++) - { - $SQ[$i] =~ s/^\@SQ\tSN:(.*?)\tLN:\d+$/$1/; - } - return(@SQ); -} - -
--- a/varscan/varscan_somatic.xml Fri Mar 07 06:17:32 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,140 +0,0 @@ -<tool id="varscan_somatic" name="VarScan Somatic (VCF Output)" version="2.3.5"> - <description> - somatic mutation caller for cancer genomics - </description> - <requirements> - <requirement type="package" version="2.3.5">VarScan</requirement> - </requirements> - <command interpreter="perl"> - - varscan_somatic.pl - "COMMAND::java -jar \$JAVA_JAR_PATH/VarScan.v2.3.5.jar somatic" - "NORMAL::$normal" - "TUMOR::$tumor" - "TUMORBAM::$tumorbam" - "OUTPUT::$output" - "LOG::$log" - - "OPTION::--min-coverage $min_coverage" - "OPTION::--min-coverage-normal $min_coverage_normal" - "OPTION::--min-coverage-tumor $min_coverage_tumor" - - "OPTION::--min-var-freq $min_var_freq" - "OPTION::--min-freq-for-hom $min_freq_for_hom" - - "OPTION::--normal-purity $normal_purity" - "OPTION::--tumor-purity $tumor_purity" - - "OPTION::--p-value $p_value" - "OPTION::--somatic-p-value $somatic_p_value" - - "OPTION::--strand-filter $strand_filter" - "OPTION::--validation $validation" - "OPTION::--output-vcf 1" - - - - </command> - - <inputs> - - <param name="normal" type="data" format="pileup" label="normal mpileup file" help="The SAMtools mpileup file for normal sample" /> - <param name="tumor" type="data" format="pileup" label="tumor mpileup file" help="The SAMtools mpileup file for tumor sample" /> - <param name="tumorbam" type="data" format="bam" label="tumor BAM file" help="The BAM file of the tumor sample used in mpileup step" /> - - <param name="min_coverage" type="integer" label="min-coverage" help="" optional="true" value="8"/> - <param name="min_coverage_normal" type="integer" label="min-coverage-normal" help="" optional="true" value="8"/> - <param name="min_coverage_tumor" type="integer" label="min-coverage-tumor" help="" optional="true" value="6"/> - - <param name="min_var_freq" type="float" label="min-var-freq" help="" optional="true" value="0.10"/> - <param name="min_freq_for_hom" type="float" label="min-freq-for-hom" help="" optional="true" value="0.75"/> - - <param name="normal_purity" type="float" label="normal-purity" help="" optional="true" value="1.00"/> - <param name="tumor_purity" type="float" label="tumor-purity" help="" optional="true" value="1.00"/> - - - <param name="p_value" type="text" label="p-value" help="" optional="true" value="0.99"/> - <param name="somatic_p_value" type="text" label="somatic-p-value" help="" optional="true" value="0.05"/> - - <param name="strand_filter" type="integer" label="strand-filter" help="" optional="true" value="1"/> - <param name="validation" type="integer" label="validation" help="" optional="true" value="0"/> - - </inputs> - <outputs> - <data type="data" format="vcf" name="output" label="${tool.name} result on ${on_string}"/> - <data type="data" format="txt" name="log" label="${tool.name} result on ${on_string} (log) "/> - <!--<data type="data" format="txt" name="snp" label="${tool.name} result on ${on_string} (SNP file)" /> - <data type="data" format="txt" name="indel" label="${tool.name} result on ${on_string} (INDEL file)" />--> - - - </outputs> - - <help> - -.. class:: infomark - -**What it does** - -:: - - VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments. The newest version, VarScan 2, is written in Java, so it runs on most operating systems. It can be used to detect different types of variation: - - Germline variants (SNPs an dindels) in individual samples or pools of samples. - Multi-sample variants (shared or private) in multi-sample datasets (with mpileup). - Somatic mutations, LOH events, and germline variants in tumor-normal pairs. - Somatic copy number alterations (CNAs) in tumor-normal exome data. - - -**Input** - -:: - - mpileup normal file - The SAMtools mpileup file for normal - mpileup tumor file - The SAMtools mpileup file for tumor - - -**Parameters** - -:: - - min-coverage - Minimum read depth at a position to make a call [8] - - min-coverage-normal - Minimum coverage in normal to call somatic [8] - - min-coverage-tumor - Minimum coverage in tumor to call somatic [6] - - min-var-freq - Minimum variant frequency to call a heterozygote [0.10] - - min-freq-for-hom - Minimum frequency to call homozygote [0.75] - - normal-purity - Estimated purity (non-tumor content) of normal sample [1.00] - - tumor-purity - Estimated purity (tumor content) of tumor sample [1.00] - - p-value - Default p-value threshold for calling variants [0.99] - - somatic-p-value - P-value threshold to call a somatic site [0.05] - - strand-filter - If set to 1, removes variants with >90% strand bias - - validation - If set to 1, outputs all compared positions even if non-variant - - output-vcf - If set to 1, outputs in VCF format [Default] - - - - </help> -</tool> -