Mercurial > repos > galaxyp > cravatool
diff test-data/Freebayes.vcf @ 1:2c7bcc1219fc draft
Updated cravatool to version 1.0 with updated formatting and new CRAVAT target URL.
| author | galaxyp |
|---|---|
| date | Thu, 16 Aug 2018 12:27:35 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Freebayes.vcf Thu Aug 16 12:27:35 2018 -0400 @@ -0,0 +1,548 @@ +##fileformat=VCFv4.2 +##fileDate=20180518 +##source=freeBayes v1.1.0-46-g8d2b3a0-dirty +##reference=/panfs/roc/rissdb/galaxy/genomes/hg38/seq/hg38.fa +##contig=<ID=chr1,length=248956422> +##contig=<ID=chr10,length=133797422> +##contig=<ID=chr11,length=135086622> +##contig=<ID=chr11_KI270721v1_random,length=100316> +##contig=<ID=chr12,length=133275309> +##contig=<ID=chr13,length=114364328> +##contig=<ID=chr14,length=107043718> +##contig=<ID=chr14_GL000009v2_random,length=201709> +##contig=<ID=chr14_GL000225v1_random,length=211173> +##contig=<ID=chr14_KI270722v1_random,length=194050> +##contig=<ID=chr14_GL000194v1_random,length=191469> +##contig=<ID=chr14_KI270723v1_random,length=38115> +##contig=<ID=chr14_KI270724v1_random,length=39555> +##contig=<ID=chr14_KI270725v1_random,length=172810> +##contig=<ID=chr14_KI270726v1_random,length=43739> 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+##contig=<ID=chr19_GL949751v2_alt,length=1002683> +##contig=<ID=chr3_KI270937v1_alt,length=165607> +##contig=<ID=chr6_GL000256v2_alt,length=4929269> +##contig=<ID=chr19_GL949752v1_alt,length=987100> +##contig=<ID=chr6_KI270758v1_alt,length=76752> +##contig=<ID=chr19_GL949753v2_alt,length=796479> +##contig=<ID=chr19_KI270938v1_alt,length=1066800> +##contig=<ID=chrM,length=16569> +##contig=<ID=chrUn_KI270302v1,length=2274> +##contig=<ID=chrUn_KI270304v1,length=2165> +##contig=<ID=chrUn_KI270303v1,length=1942> +##contig=<ID=chrUn_KI270305v1,length=1472> +##contig=<ID=chrUn_KI270322v1,length=21476> +##contig=<ID=chrUn_KI270320v1,length=4416> +##contig=<ID=chrUn_KI270310v1,length=1201> +##contig=<ID=chrUn_KI270316v1,length=1444> +##contig=<ID=chrUn_KI270315v1,length=2276> +##contig=<ID=chrUn_KI270312v1,length=998> +##contig=<ID=chrUn_KI270311v1,length=12399> +##contig=<ID=chrUn_KI270317v1,length=37690> +##contig=<ID=chrUn_KI270412v1,length=1179> +##contig=<ID=chrUn_KI270411v1,length=2646> +##contig=<ID=chrUn_KI270414v1,length=2489> +##contig=<ID=chrUn_KI270419v1,length=1029> +##contig=<ID=chrUn_KI270418v1,length=2145> +##contig=<ID=chrUn_KI270420v1,length=2321> +##contig=<ID=chrUn_KI270424v1,length=2140> +##contig=<ID=chrUn_KI270417v1,length=2043> +##contig=<ID=chrUn_KI270422v1,length=1445> +##contig=<ID=chrUn_KI270423v1,length=981> +##contig=<ID=chrUn_KI270425v1,length=1884> +##contig=<ID=chrUn_KI270429v1,length=1361> +##contig=<ID=chrUn_KI270442v1,length=392061> +##contig=<ID=chrUn_KI270466v1,length=1233> +##contig=<ID=chrUn_KI270465v1,length=1774> +##contig=<ID=chrUn_KI270467v1,length=3920> +##contig=<ID=chrUn_KI270435v1,length=92983> +##contig=<ID=chrUn_KI270438v1,length=112505> +##contig=<ID=chrUn_KI270468v1,length=4055> +##contig=<ID=chrUn_KI270510v1,length=2415> +##contig=<ID=chrUn_KI270509v1,length=2318> +##contig=<ID=chrUn_KI270518v1,length=2186> +##contig=<ID=chrUn_KI270508v1,length=1951> +##contig=<ID=chrUn_KI270516v1,length=1300> +##contig=<ID=chrUn_KI270512v1,length=22689> +##contig=<ID=chrUn_KI270519v1,length=138126> +##contig=<ID=chrUn_KI270522v1,length=5674> +##contig=<ID=chrUn_KI270511v1,length=8127> +##contig=<ID=chrUn_KI270515v1,length=6361> +##contig=<ID=chrUn_KI270507v1,length=5353> +##contig=<ID=chrUn_KI270517v1,length=3253> +##contig=<ID=chrUn_KI270529v1,length=1899> +##contig=<ID=chrUn_KI270528v1,length=2983> +##contig=<ID=chrUn_KI270530v1,length=2168> +##contig=<ID=chrUn_KI270539v1,length=993> +##contig=<ID=chrUn_KI270538v1,length=91309> +##contig=<ID=chrUn_KI270544v1,length=1202> +##contig=<ID=chrUn_KI270548v1,length=1599> +##contig=<ID=chrUn_KI270583v1,length=1400> +##contig=<ID=chrUn_KI270587v1,length=2969> +##contig=<ID=chrUn_KI270580v1,length=1553> +##contig=<ID=chrUn_KI270581v1,length=7046> +##contig=<ID=chrUn_KI270579v1,length=31033> +##contig=<ID=chrUn_KI270589v1,length=44474> +##contig=<ID=chrUn_KI270590v1,length=4685> +##contig=<ID=chrUn_KI270584v1,length=4513> +##contig=<ID=chrUn_KI270582v1,length=6504> +##contig=<ID=chrUn_KI270588v1,length=6158> +##contig=<ID=chrUn_KI270593v1,length=3041> +##contig=<ID=chrUn_KI270591v1,length=5796> +##contig=<ID=chrUn_KI270330v1,length=1652> +##contig=<ID=chrUn_KI270329v1,length=1040> +##contig=<ID=chrUn_KI270334v1,length=1368> +##contig=<ID=chrUn_KI270333v1,length=2699> +##contig=<ID=chrUn_KI270335v1,length=1048> +##contig=<ID=chrUn_KI270338v1,length=1428> +##contig=<ID=chrUn_KI270340v1,length=1428> +##contig=<ID=chrUn_KI270336v1,length=1026> +##contig=<ID=chrUn_KI270337v1,length=1121> +##contig=<ID=chrUn_KI270363v1,length=1803> +##contig=<ID=chrUn_KI270364v1,length=2855> +##contig=<ID=chrUn_KI270362v1,length=3530> +##contig=<ID=chrUn_KI270366v1,length=8320> +##contig=<ID=chrUn_KI270378v1,length=1048> +##contig=<ID=chrUn_KI270379v1,length=1045> +##contig=<ID=chrUn_KI270389v1,length=1298> +##contig=<ID=chrUn_KI270390v1,length=2387> +##contig=<ID=chrUn_KI270387v1,length=1537> +##contig=<ID=chrUn_KI270395v1,length=1143> +##contig=<ID=chrUn_KI270396v1,length=1880> +##contig=<ID=chrUn_KI270388v1,length=1216> +##contig=<ID=chrUn_KI270394v1,length=970> +##contig=<ID=chrUn_KI270386v1,length=1788> +##contig=<ID=chrUn_KI270391v1,length=1484> +##contig=<ID=chrUn_KI270383v1,length=1750> +##contig=<ID=chrUn_KI270393v1,length=1308> +##contig=<ID=chrUn_KI270384v1,length=1658> +##contig=<ID=chrUn_KI270392v1,length=971> +##contig=<ID=chrUn_KI270381v1,length=1930> +##contig=<ID=chrUn_KI270385v1,length=990> +##contig=<ID=chrUn_KI270382v1,length=4215> +##contig=<ID=chrUn_KI270376v1,length=1136> +##contig=<ID=chrUn_KI270374v1,length=2656> +##contig=<ID=chrUn_KI270372v1,length=1650> +##contig=<ID=chrUn_KI270373v1,length=1451> +##contig=<ID=chrUn_KI270375v1,length=2378> +##contig=<ID=chrUn_KI270371v1,length=2805> +##contig=<ID=chrUn_KI270448v1,length=7992> +##contig=<ID=chrUn_KI270521v1,length=7642> +##contig=<ID=chrUn_GL000195v1,length=182896> +##contig=<ID=chrUn_GL000219v1,length=179198> +##contig=<ID=chrUn_GL000220v1,length=161802> +##contig=<ID=chrUn_GL000224v1,length=179693> +##contig=<ID=chrUn_KI270741v1,length=157432> +##contig=<ID=chrUn_GL000226v1,length=15008> +##contig=<ID=chrUn_GL000213v1,length=164239> +##contig=<ID=chrUn_KI270743v1,length=210658> +##contig=<ID=chrUn_KI270744v1,length=168472> +##contig=<ID=chrUn_KI270745v1,length=41891> +##contig=<ID=chrUn_KI270746v1,length=66486> +##contig=<ID=chrUn_KI270747v1,length=198735> +##contig=<ID=chrUn_KI270748v1,length=93321> +##contig=<ID=chrUn_KI270749v1,length=158759> +##contig=<ID=chrUn_KI270750v1,length=148850> +##contig=<ID=chrUn_KI270751v1,length=150742> +##contig=<ID=chrUn_KI270752v1,length=27745> +##contig=<ID=chrUn_KI270753v1,length=62944> +##contig=<ID=chrUn_KI270754v1,length=40191> +##contig=<ID=chrUn_KI270755v1,length=36723> +##contig=<ID=chrUn_KI270756v1,length=79590> +##contig=<ID=chrUn_KI270757v1,length=71251> +##contig=<ID=chrUn_GL000214v1,length=137718> +##contig=<ID=chrUn_KI270742v1,length=186739> +##contig=<ID=chrUn_GL000216v2,length=176608> +##contig=<ID=chrUn_GL000218v1,length=161147> +##contig=<ID=chrX,length=156040895> +##contig=<ID=chrY,length=57227415> +##contig=<ID=chrY_KI270740v1_random,length=37240> +##phasing=none +##commandline="freebayes --region chrY_KI270740v1_random:0..37240 --bam b_0.bam --fasta-reference /panfs/roc/rissdb/galaxy/genomes/hg38/seq/hg38.fa --vcf ./vcf_output/part_chrY_KI270740v1_random:0..37240.vcf" +##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus"> +##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype"> +##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes"> +##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> +##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]"> +##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype."> +##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype."> +##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally"> +##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally"> +##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred"> +##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred"> +##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations"> +##INFO=<ID=PQA,Number=A,Type=Float,Description="Alternate allele quality sum in phred for partial observations"> +##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand"> +##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand"> +##INFO=<ID=SAF,Number=A,Type=Integer,Description="Number of alternate observations on the forward strand"> +##INFO=<ID=SAR,Number=A,Type=Integer,Description="Number of alternate observations on the reverse strand"> +##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous"> +##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome"> +##INFO=<ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=RPL,Number=A,Type=Float,Description="Reads Placed Left: number of reads supporting the alternate balanced to the left (5') of the alternate allele"> +##INFO=<ID=RPR,Number=A,Type=Float,Description="Reads Placed Right: number of reads supporting the alternate balanced to the right (3') of the alternate allele"> +##INFO=<ID=EPP,Number=A,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=DPRA,Number=A,Type=Float,Description="Alternate allele depth ratio. Ratio between depth in samples with each called alternate allele and those without."> +##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best."> +##INFO=<ID=GTI,Number=1,Type=Integer,Description="Number of genotyping iterations required to reach convergence or bailout."> +##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex."> +##INFO=<ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing. Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR."> +##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position."> +##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles."> +##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length"> +##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles"> +##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles"> +##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments"> +##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments"> +##INFO=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block."> +##INFO=<ID=END,Number=1,Type=Integer,Description="Last position (inclusive) in gVCF output record."> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype"> +##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> +##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Number of observation for each allele"> +##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count"> +##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations"> +##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count"> +##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations"> +##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block."> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT unknown +chr1 156701052 . C T 122.853 . AB=0.4;ABP=4.74748;AC=1;AF=0.5;AN=2;AO=8;CIGAR=1X;DP=20;DPB=20;DPRA=0;EPP=4.09604;EPPR=4.45795;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=11.0181;PAIRED=1;PAIREDR=0.833333;PAO=0;PQA=0;PQR=0;PRO=0;QA=255;QR=217;RO=6;RPL=0;RPP=20.3821;RPPR=4.45795;RPR=8;RUN=1;SAF=5;SAP=4.09604;SAR=3;SRF=6;SRP=16.0391;SRR=0;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:20:6,8:6:217:8:255:-18.7505,0,-15.3493 +chr1 156701053 . CT AG 24.1256 . AB=0.666667;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=2;CIGAR=2X;DP=3;DPB=4;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=2;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=2.97054;PAIRED=0.5;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=2;QA=72;QR=38;RO=1;RPL=0;RPP=7.35324;RPPR=5.18177;RPR=2;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=1;SRP=5.18177;SRR=0;TYPE=complex GT:DP:AD:RO:QR:AO:QA:GL 0/1:3:1,2:1:38:2:72:-5.33122,0,-2.03897 +chr1 156705422 . T C 126013 . AB=0.318664;ABP=5149.54;AC=1;AF=0.5;AN=2;AO=5742;CIGAR=1X;DP=18019;DPB=18019;DPRA=0;EPP=282.707;EPPR=1125.45;GTI=0;LEN=1;MEANALT=3;MQM=59.9692;MQMR=59.9856;NS=1;NUMALT=1;ODDS=29015.6;PAIRED=0.984674;PAIREDR=0.981657;PAO=0;PQA=0;PQR=0;PRO=0;QA=208149;QR=444948;RO=12266;RPL=3615;RPP=840.341;RPPR=1076.08;RPR=2127;RUN=1;SAF=3392;SAP=413.618;SAR=2350;SRF=6908;SRP=428.329;SRR=5358;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:18019:12266,5742:12266:444948:5742:208149:-13290.6,0,-34589.6 +chr11 27889736 . C T 52.1986 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=7.35324;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=7.37776;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=74;QR=0;RO=0;RPL=0;RPP=7.35324;RPPR=0;RPR=2;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 1/1:2:0,2:0:0:2:74:-7.02577,-0.60206,0 +chr11 27889762 . T A 35.1213 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=7.35324;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=7.37776;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=56;QR=0;RO=0;RPL=2;RPP=7.35324;RPPR=0;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 1/1:2:0,2:0:0:2:56:-5.31791,-0.60206,0 +chr11 27889795 . T C 295.783 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=16;CIGAR=1X;DP=18;DPB=18;DPRA=0;EPP=29.6108;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=22.1246;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=471;QR=30;RO=2;RPL=0;RPP=37.7539;RPPR=7.35324;RPR=16;RUN=1;SAF=1;SAP=29.6108;SAR=15;SRF=2;SRP=7.35324;SRR=0;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 1/1:18:2,16:2:30:16:471:-39.8133,-2.56857,0 +chr11 27889819 . A G 765.194 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=32;CIGAR=1X;DP=33;DPB=33;DPRA=0;EPP=9.79615;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=48.9666;PAIRED=0.03125;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=990;QR=0;RO=0;RPL=0;RPP=72.4974;RPPR=0;RPR=32;RUN=1;SAF=11;SAP=9.79615;SAR=21;SRF=0;SRP=0;SRR=0;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 1/1:33:0,32:0:0:32:990:-89.197,-9.63296,0 +chr11 27889843 . A T 948.794 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=35;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=8.03571;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=49.5538;PAIRED=0.0571429;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1109;QR=15;RO=1;RPL=12;RPP=10.5174;RPPR=5.18177;RPR=23;RUN=1;SAF=12;SAP=10.5174;SAR=23;SRF=0;SRP=5.18177;SRR=1;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 1/1:36:1,35:1:15:35:1109:-98.5725,-9.33709,0 +chr11 27889860 . C T 170.937 . AB=0.325;ABP=13.6505;AC=1;AF=0.5;AN=2;AO=13;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=3.17734;EPPR=9.52472;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=39.3596;PAIRED=0.153846;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=390;QR=888;RO=27;RPL=8;RPP=4.51363;RPPR=12.7417;RPR=5;RUN=1;SAF=8;SAP=4.51363;SAR=5;SRF=5;SRP=26.2531;SRR=22;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:40:27,13:27:888:13:390:-23.341,0,-68.1636 +chr11 27889934 . T A 75.8995 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=3;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=3.73412;EPPR=7.35324;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=6.74621;PAIRED=0.333333;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=114;QR=32;RO=2;RPL=3;RPP=9.52472;RPPR=7.35324;RPR=0;RUN=1;SAF=1;SAP=3.73412;SAR=2;SRF=0;SRP=7.35324;SRR=2;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:6:2,3:2:32:3:114:-8.91977,0,-1.38149 +chr12 6560786 . A C,T 0.671284 . AB=0.333333,0.388889;ABP=7.35324,4.9405;AC=1,0;AF=0.5,0;AN=2;AO=6,7;CIGAR=1X,1X;DP=18;DPB=18;DPRA=0,0;EPP=16.0391,3.32051;EPPR=3.0103;GTI=0;LEN=1,1;MEANALT=3,3;MQM=60,51.5714;MQMR=60;NS=1;NUMALT=2;ODDS=2.30652;PAIRED=1,1;PAIREDR=1;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=90,100;QR=76;RO=2;RPL=0,0;RPP=16.0391,18.2106;RPPR=3.0103;RPR=6,7;RUN=1,1;SAF=0,3;SAP=16.0391,3.32051;SAR=6,4;SRF=2;SRP=7.35324;SRR=0;TYPE=snp,snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:18:2,6,7:2:76:6,7:90,100:-5.69842,0,-4.46814,-0.502973,-0.533287,-4.67076 +chr12 6561055 . T C 14340.8 . AB=0.235264;ABP=2357.67;AC=1;AF=0.5;AN=2;AO=910;CIGAR=1X;DP=3868;DPB=3868;DPRA=0;EPP=7.21962;EPPR=59.3944;GTI=0;LEN=1;MEANALT=2;MQM=59.9352;MQMR=59.7205;NS=1;NUMALT=1;ODDS=3302.08;PAIRED=0.983516;PAIREDR=0.990186;PAO=0;PQA=0;PQR=0;PRO=0;QA=33224;QR=106496;RO=2955;RPL=107;RPP=1158.94;RPPR=4030.18;RPR=803;RUN=1;SAF=481;SAP=9.46268;SAR=429;SRF=1663;SRP=104.155;SRR=1292;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:3868:2955,910:2955:106496:910:33224:-1821.72,0,-8372.79 +chr12 110033192 . T C 53.1444 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=7.35324;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=7.37776;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=0;RO=0;RPL=0;RPP=7.35324;RPPR=0;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=0;SRP=0;SRR=0;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 1/1:2:0,2:0:0:2:75:-7.12034,-0.60206,0 +chr12 110339630 . C T 48828.1 . AB=0.268901;ABP=4224.36;AC=1;AF=0.5;AN=2;AO=2447;CIGAR=1X;DP=9100;DPB=9100;DPRA=0;EPP=710.668;EPPR=1883.3;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=11243.1;PAIRED=0.985288;PAIREDR=0.980156;PAO=0;PQA=0;PQR=0;PRO=0;QA=90595;QR=244569;RO=6652;RPL=1094;RPP=62.5381;RPPR=155.737;RPR=1353;RUN=1;SAF=1227;SAP=3.05378;SAR=1220;SRF=3354;SRP=4.03401;SRR=3298;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:9100:6652,2447:6652:244569:2447:90595:-5409.03,0,-19257.6 +chr14 94079142 . T C 0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=756;CIGAR=1X;DP=3707;DPB=3707;DPRA=0;EPP=71.1302;EPPR=383.929;GTI=0;LEN=1;MEANALT=3;MQM=23.164;MQMR=22.8823;NS=1;NUMALT=1;ODDS=1140.53;PAIRED=0.994709;PAIREDR=0.99491;PAO=0;PQA=0;PQR=0;PRO=0;QA=27331;QR=106693;RO=2947;RPL=419;RPP=22.3238;RPPR=516.755;RPR=337;RUN=1;SAF=312;SAP=53.0576;SAR=444;SRF=1285;SRP=107.737;SRR=1662;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/0:3707:2947,756:2947:106693:756:27331:0,-172.332,-2685.28 +chr14 102011985 . A T 12962.3 . AB=0.301267;ABP=734.044;AC=1;AF=0.5;AN=2;AO=642;CIGAR=1X;DP=2131;DPB=2131;DPRA=0;EPP=6.47383;EPPR=23.6897;GTI=0;LEN=1;MEANALT=3;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=2984.69;PAIRED=0.995327;PAIREDR=0.98117;PAO=0;PQA=0;PQR=0;PRO=0;QA=22490;QR=51005;RO=1487;RPL=362;RPP=25.7533;RPPR=15.6405;RPR=280;RUN=1;SAF=307;SAP=5.66207;SAR=335;SRF=729;SRP=4.23842;SRR=758;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:2131:1487,642:1487:51005:642:22490:-1382.22,0,-3947.19 +chr14 102083954 . C T 240741 . AB=0.203722;ABP=65019.6;AC=1;AF=0.5;AN=2;AO=17372;CIGAR=1X;DP=85273;DPB=85273;DPRA=0;EPP=2106.28;EPPR=12892.8;GTI=0;LEN=1;MEANALT=3;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=55432.6;PAIRED=0.982155;PAIREDR=0.980402;PAO=0;PQA=0;PQR=0;PRO=0;QA=637523;QR=2489236;RO=67865;RPL=5766;RPP=4266.16;RPPR=13677.6;RPR=11606;RUN=1;SAF=9063;SAP=74.0739;SAR=8309;SRF=35817;SRP=457.538;SRR=32048;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:85273:67865,17372:67865:2489236:17372:637523:-31680.6,0,-198225 +chr14 102084466 . G A 866755 . AB=0.793643;ABP=29738.6;AC=1;AF=0.5;AN=2;AO=31510;CIGAR=1X;DP=39703;DPB=39703;DPRA=0;EPP=3701.63;EPPR=962.263;GTI=0;LEN=1;MEANALT=3;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=26239.5;PAIRED=0.994319;PAIREDR=0.994371;PAO=0;PQA=0;PQR=0;PRO=0;QA=1162876;QR=302820;RO=8172;RPL=24066;RPP=19043.3;RPPR=4663.58;RPR=7444;RUN=1;SAF=11974;SAP=3943.76;SAR=19536;SRF=3044;SRP=1157.05;SRR=5128;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:39703:8172,31510:8172:302820:31510:1162876:-92643.6,0,-15290.2 +chr17 82082413 . A C 0.015243 . AB=0.444444;ABP=3.25157;AC=1;AF=0.5;AN=2;AO=4;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=5.18177;EPPR=3.44459;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=5.65043;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=57;QR=158;RO=5;RPL=0;RPP=11.6962;RPPR=6.91895;RPR=4;RUN=1;SAF=1;SAP=5.18177;SAR=3;SRF=4;SRP=6.91895;SRR=1;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:9:5,4:5:158:4:57:-2.56319,0,-11.821 +chr17 82082414 . C G 0.0150561 . AB=0.4;ABP=3.44459;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=7.35324;EPPR=9.52472;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=5.66308;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=29;QR=110;RO=3;RPL=1;RPP=3.0103;RPPR=9.52472;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=3;SRP=9.52472;SRR=0;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:5:3,2:3:110:2:29:-1.24983,0,-8.7554 +chr17 82082606 . C T 10374.8 . AB=0.202823;ABP=2937.89;AC=1;AF=0.5;AN=2;AO=776;CIGAR=1X;DP=3826;DPB=3826;DPRA=0;EPP=22.755;EPPR=126.853;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=59.9806;NS=1;NUMALT=1;ODDS=2388.89;PAIRED=0.981959;PAIREDR=0.985569;PAO=0;PQA=0;PQR=0;PRO=0;QA=27982;QR=110520;RO=3049;RPL=338;RPP=30.9932;RPPR=253.452;RPR=438;RUN=1;SAF=422;SAP=15.9496;SAR=354;SRF=1759;SRP=159.665;SRR=1290;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:3826:3049,776:3049:110520:776:27982:-1365.58,0,-8788 +chr17 82082731 . T C 701.469 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=26;CIGAR=1X;DP=26;DPB=26;DPRA=0;EPP=15.0369;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=40.6488;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=888;QR=0;RO=0;RPL=22;RPP=30.0702;RPPR=0;RPR=4;RUN=1;SAF=3;SAP=36.4176;SAR=23;SRF=0;SRP=0;SRR=0;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 1/1:26:0,26:0:0:26:888:-80.2195,-7.82678,0 +chr17 82082763 . G A 91.2949 . AB=0.6;ABP=3.87889;AC=1;AF=0.5;AN=2;AO=6;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=16.0391;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=11.9868;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=221;QR=144;RO=4;RPL=6;RPP=16.0391;RPPR=5.18177;RPR=0;RUN=1;SAF=0;SAP=16.0391;SAR=6;SRF=0;SRP=11.6962;SRR=4;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:10:4,6:4:144:6:221:-17.2361,0,-10.3021 +chr19 17205335 . A T 0.00158993 . AB=0.285714;ABP=5.80219;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=7;DPB=7;DPRA=0;EPP=3.0103;EPPR=6.91895;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=48.2;NS=1;NUMALT=1;ODDS=7.91247;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=28;QR=169;RO=5;RPL=0;RPP=7.35324;RPPR=13.8677;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=1;SRP=6.91895;SRR=4;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:7:5,2:5:169:2:28:-0.55277,0,-10.4001 +chr19 17205444 . T C 206.198 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=7;CIGAR=1X;DP=7;DPB=7;DPRA=0;EPP=5.80219;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=14.3092;PAIRED=0.857143;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=249;QR=0;RO=0;RPL=2;RPP=5.80219;RPPR=0;RPR=5;RUN=1;SAF=4;SAP=3.32051;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 1/1:7:0,7:0:0:7:249:-22.753,-2.10721,0 +chr19 17205973 . T C 12243.8 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=406;CIGAR=1X;DP=406;DPB=406;DPRA=0;EPP=14.3276;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=58.4015;MQMR=0;NS=1;NUMALT=1;ODDS=567.441;PAIRED=0.985222;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=14833;QR=0;RO=0;RPL=368;RPP=585.457;RPPR=0;RPR=38;RUN=1;SAF=182;SAP=12.445;SAR=224;SRF=0;SRP=0;SRR=0;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 1/1:406:0,406:0:0:406:14833:-1297.85,-122.218,0 +chr19 18856059 . C T 10269.5 . AB=0.248844;ABP=1306.46;AC=1;AF=0.5;AN=2;AO=592;CIGAR=1X;DP=2379;DPB=2379;DPRA=0;EPP=30.139;EPPR=172.262;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=59.9339;NS=1;NUMALT=1;ODDS=2364.65;PAIRED=0.991554;PAIREDR=0.983754;PAO=0;PQA=0;PQR=0;PRO=0;QA=21546;QR=64865;RO=1785;RPL=120;RPP=457.494;RPPR=1043.89;RPR=472;RUN=1;SAF=303;SAP=3.72923;SAR=289;SRF=873;SRP=4.86061;SRR=912;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:2379:1785,592:1785:64865:592:21546:-1222.54,0,-5112.92 +chr19 18867128 . G C 398.913 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=14;CIGAR=1X;DP=14;DPB=14;DPRA=0;EPP=33.4109;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=24.0133;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=523;QR=0;RO=0;RPL=11;RPP=12.937;RPPR=0;RPR=3;RUN=1;SAF=11;SAP=12.937;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 1/1:14:0,14:0:0:14:523:-47.4124,-4.21442,0 +chr2 231456129 . GGATGGCT TGATTCAC 54.047 . AB=0.363636;ABP=4.78696;AC=1;AF=0.5;AN=2;AO=4;CIGAR=1X3M4X;DP=11;DPB=12.375;DPRA=0;EPP=3.0103;EPPR=5.80219;GTI=0;LEN=8;MEANALT=1;MQM=60;MQMR=51.5714;NS=1;NUMALT=1;ODDS=12.4448;PAIRED=1;PAIREDR=0.714286;PAO=0;PQA=0;PQR=134;PRO=4;QA=150;QR=252;RO=7;RPL=0;RPP=11.6962;RPPR=18.2106;RPR=4;RUN=1;SAF=2;SAP=3.0103;SAR=2;SRF=5;SRP=5.80219;SRR=2;TYPE=complex GT:DP:AD:RO:QR:AO:QA:GL 0/1:11:7,4:7:252:4:150:-9.35048,0,-24.4716 +chr2 231456762 . T C 60.9983 . AB=0.333333;ABP=7.35324;AC=1;AF=0.5;AN=2;AO=6;CIGAR=1X;DP=18;DPB=18;DPRA=0;EPP=3.0103;EPPR=9.52472;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=14.0454;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=181;QR=429;RO=12;RPL=0;RPP=16.0391;RPPR=29.068;RPR=6;RUN=1;SAF=3;SAP=3.0103;SAR=3;SRF=9;SRP=9.52472;SRR=3;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:18:12,6:12:429:6:181:-11.1631,0,-33.5255 +chr2 231456763 . A G 0.000241075 . AB=0.25;ABP=9.52472;AC=1;AF=0.5;AN=2;AO=3;CIGAR=1X;DP=12;DPB=12;DPRA=0;EPP=9.52472;EPPR=18.2106;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=9.79893;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=257;RO=7;RPL=0;RPP=9.52472;RPPR=18.2106;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=7;SRP=18.2106;SRR=0;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:12:7,3:7:257:3:39:-0.481678,0,-20.2656 +chr2 231456764 . C T 67.7463 . AB=0.714286;ABP=5.80219;AC=1;AF=0.5;AN=2;AO=5;CIGAR=1X;DP=7;DPB=7;DPRA=0;EPP=13.8677;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=3.26857;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=166;QR=76;RO=2;RPL=0;RPP=13.8677;RPPR=7.35324;RPR=5;RUN=1;SAF=5;SAP=13.8677;SAR=0;SRF=2;SRP=7.35324;SRR=0;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:7:2,5:2:76:5:166:-13.1558,0,-5.1076 +chr2 231457190 . T C 744.752 . AB=0.221739;ABP=157.695;AC=1;AF=0.5;AN=2;AO=51;CIGAR=1X;DP=230;DPB=230;DPRA=0;EPP=3.3935;EPPR=7.38964;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=171.486;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=1858;QR=6693;RO=179;RPL=34;RPP=15.3153;RPPR=25.4408;RPR=17;RUN=1;SAF=18;SAP=12.5903;SAR=33;SRF=84;SRP=4.47817;SRR=95;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:230:179,51:179:6693:51:1858:-98.2392,0,-533.104