Mercurial > repos > iuc > gemini_burden
view test-data/util/build-data/test.comp_het.vcf @ 7:df57188562f0 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
| author | iuc |
|---|---|
| date | Tue, 10 Mar 2020 06:17:40 -0400 |
| parents | c70d79e0eed7 |
| children |
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##fileformat=VCFv4.1 ##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> ##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"> ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed"> ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> ##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"> ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> ##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?"> ##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions"> ##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias"> ##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction"> ##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes"> ##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation"> ##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"> ##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads"> ##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities"> ##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth"> ##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias"> ##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[bam/all.bam] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=/home/arq5x/cphg-home/shared/genomes/hg19/bwa/gatk/human_g1k_v37.fasta rodBind=[] nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=20 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=BOTH p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=DISCOVERY output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 computeSLOD=false alleles=(RodBinding name= source=UNBOUND) min_base_quality_score=17 max_deletion_fraction=0.05 multiallelic=false max_alternate_alleles=5 min_indel_count_for_genotyping=5 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=45.0 indelHaplotypeSize=80 bandedIndel=false indelDebug=false ignoreSNPAlleles=false dbsnp=(RodBinding name= source=UNBOUND) out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_mismatching_base_and_quals=false" ##contig=<ID=1,length=249250621,assembly=b37> ##contig=<ID=10,length=135534747,assembly=b37> ##contig=<ID=11,length=135006516,assembly=b37> ##contig=<ID=12,length=133851895,assembly=b37> ##contig=<ID=13,length=115169878,assembly=b37> ##contig=<ID=14,length=107349540,assembly=b37> ##contig=<ID=15,length=102531392,assembly=b37> ##contig=<ID=16,length=90354753,assembly=b37> ##contig=<ID=17,length=81195210,assembly=b37> ##contig=<ID=18,length=78077248,assembly=b37> ##contig=<ID=19,length=59128983,assembly=b37> ##contig=<ID=2,length=243199373,assembly=b37> ##contig=<ID=20,length=63025520,assembly=b37> ##contig=<ID=21,length=48129895,assembly=b37> ##contig=<ID=22,length=51304566,assembly=b37> ##contig=<ID=3,length=198022430,assembly=b37> ##contig=<ID=4,length=191154276,assembly=b37> ##contig=<ID=5,length=180915260,assembly=b37> ##contig=<ID=6,length=171115067,assembly=b37> ##contig=<ID=7,length=159138663,assembly=b37> ##contig=<ID=8,length=146364022,assembly=b37> ##contig=<ID=9,length=141213431,assembly=b37> ##contig=<ID=GL000191.1,length=106433,assembly=b37> ##contig=<ID=GL000192.1,length=547496,assembly=b37> ##contig=<ID=GL000193.1,length=189789,assembly=b37> ##contig=<ID=GL000194.1,length=191469,assembly=b37> ##contig=<ID=GL000195.1,length=182896,assembly=b37> ##contig=<ID=GL000196.1,length=38914,assembly=b37> ##contig=<ID=GL000197.1,length=37175,assembly=b37> ##contig=<ID=GL000198.1,length=90085,assembly=b37> ##contig=<ID=GL000199.1,length=169874,assembly=b37> ##contig=<ID=GL000200.1,length=187035,assembly=b37> ##contig=<ID=GL000201.1,length=36148,assembly=b37> ##contig=<ID=GL000202.1,length=40103,assembly=b37> ##contig=<ID=GL000203.1,length=37498,assembly=b37> ##contig=<ID=GL000204.1,length=81310,assembly=b37> ##contig=<ID=GL000205.1,length=174588,assembly=b37> ##contig=<ID=GL000206.1,length=41001,assembly=b37> ##contig=<ID=GL000207.1,length=4262,assembly=b37> ##contig=<ID=GL000208.1,length=92689,assembly=b37> ##contig=<ID=GL000209.1,length=159169,assembly=b37> ##contig=<ID=GL000210.1,length=27682,assembly=b37> ##contig=<ID=GL000211.1,length=166566,assembly=b37> ##contig=<ID=GL000212.1,length=186858,assembly=b37> ##contig=<ID=GL000213.1,length=164239,assembly=b37> ##contig=<ID=GL000214.1,length=137718,assembly=b37> ##contig=<ID=GL000215.1,length=172545,assembly=b37> ##contig=<ID=GL000216.1,length=172294,assembly=b37> ##contig=<ID=GL000217.1,length=172149,assembly=b37> ##contig=<ID=GL000218.1,length=161147,assembly=b37> ##contig=<ID=GL000219.1,length=179198,assembly=b37> ##contig=<ID=GL000220.1,length=161802,assembly=b37> ##contig=<ID=GL000221.1,length=155397,assembly=b37> ##contig=<ID=GL000222.1,length=186861,assembly=b37> ##contig=<ID=GL000223.1,length=180455,assembly=b37> ##contig=<ID=GL000224.1,length=179693,assembly=b37> ##contig=<ID=GL000225.1,length=211173,assembly=b37> ##contig=<ID=GL000226.1,length=15008,assembly=b37> ##contig=<ID=GL000227.1,length=128374,assembly=b37> ##contig=<ID=GL000228.1,length=129120,assembly=b37> ##contig=<ID=GL000229.1,length=19913,assembly=b37> ##contig=<ID=GL000230.1,length=43691,assembly=b37> ##contig=<ID=GL000231.1,length=27386,assembly=b37> ##contig=<ID=GL000232.1,length=40652,assembly=b37> ##contig=<ID=GL000233.1,length=45941,assembly=b37> ##contig=<ID=GL000234.1,length=40531,assembly=b37> ##contig=<ID=GL000235.1,length=34474,assembly=b37> ##contig=<ID=GL000236.1,length=41934,assembly=b37> ##contig=<ID=GL000237.1,length=45867,assembly=b37> ##contig=<ID=GL000238.1,length=39939,assembly=b37> ##contig=<ID=GL000239.1,length=33824,assembly=b37> ##contig=<ID=GL000240.1,length=41933,assembly=b37> ##contig=<ID=GL000241.1,length=42152,assembly=b37> ##contig=<ID=GL000242.1,length=43523,assembly=b37> ##contig=<ID=GL000243.1,length=43341,assembly=b37> ##contig=<ID=GL000244.1,length=39929,assembly=b37> ##contig=<ID=GL000245.1,length=36651,assembly=b37> ##contig=<ID=GL000246.1,length=38154,assembly=b37> ##contig=<ID=GL000247.1,length=36422,assembly=b37> ##contig=<ID=GL000248.1,length=39786,assembly=b37> ##contig=<ID=GL000249.1,length=38502,assembly=b37> ##contig=<ID=MT,length=16569,assembly=b37> ##contig=<ID=X,length=155270560,assembly=b37> ##contig=<ID=Y,length=59373566,assembly=b37> ##reference=file:///home/arq5x/cphg-home/shared/genomes/hg19/bwa/gatk/human_g1k_v37.fasta ##SnpEffVersion="SnpEff 3.2 (build 2013-03-14), by Pablo Cingolani" ##SnpEffCmd="SnpEff -i vcf -o vcf GRCh37.66 /if2/arq5x/cphg-quinlan/projects/sms-elsea/varCalling/all.vcf " ##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_change| Amino_Acid_length | Gene_Name | Gene_BioType | Coding | Transcript | Exon | GenotypeNum [ | ERRORS | WARNINGS ] )' "> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT child_1 child_2 dad_2 mom_2 dad_1 mom_1 child_3 dad_3 mom_3 child_4 dad_4 mom_4 1 16977 . G A 2022.88 . AC=9;AF=0.375;AN=24;BaseQRankSum=-25.424;DP=2999;DS;Dels=0.00;FS=4.077;HRun=0;HaplotypeScore=1.6017;InbreedingCoeff=-0.5953;MQ=10.20;MQ0=124;MQRankSum=0.084;QD=0.90;ReadPosRankSum=0.727;EFF=DOWNSTREAM(MODIFIER|||||DDX11L1|processed_transcript|NON_CODING|ENST00000456328||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655||1),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492||1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|6|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|7|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|7|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|6|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|7|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|7|1) GT:AD:DP:GQ:PL 0/1:181,69:250:4.24:4,0,401 0/0:190,60:250:5.21:0,5,708 0/1:167,83:250:72.66:73,0,721 0/0:187,63:250:63.12:0,63,633 0/0:221,29:250:96.57:0,97,1729 0/1:160,90:250:99:175,0,537 0/1:177,73:250:99:412,0,723 0/1:183,67:250:99:209,0,838 0/1:174,76:250:99:284,0,844 0/1:194,53:248:26.15:26,0,756 0/1:149,101:250:99:681,0,496 0/1:184,66:250:99:229,0,561 1 17222 . A G 225.47 . AC=4;AF=0.167;AN=24;BaseQRankSum=-1.725;DP=2985;DS;Dels=0.00;FS=6.073;HRun=0;HaplotypeScore=1.1157;InbreedingCoeff=-0.2212;MQ=14.57;MQ0=605;MQRankSum=-3.790;QD=0.23;ReadPosRankSum=1.860;EFF=DOWNSTREAM(MODIFIER|||||DDX11L1|processed_transcript|NON_CODING|ENST00000456328||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655||1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|5|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|8|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|6|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|6|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|5|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|6|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|6|1) GT:AD:DP:GQ:PL 0/0:224,25:250:44.94:0,45,987 0/1:190,44:241:55.80:56,0,776 0/0:230,17:250:90.16:0,90,940 0/1:212,34:250:36.11:36,0,754 0/0:191,55:248:18.04:0,18,1324 0/0:232,17:250:84.90:0,85,1270 0/0:223,27:250:99:0,129,1563 0/0:237,13:250:99:0,107,1537 0/1:207,42:249:99:106,0,1096 0/1:204,43:247:91.42:91,0,1280 0/0:229,20:249:99:0,113,1404 0/0:221,29:250:3.04:0,3,1183 1 17363 . TTCT T 628.85 . AC=2;AF=0.083;AN=24;BaseQRankSum=4.577;DP=2951;DS;FS=10.112;HRun=0;HaplotypeScore=316.7300;InbreedingCoeff=-0.0909;MQ=22.73;MQ0=27;MQRankSum=1.681;QD=1.33;ReadPosRankSum=0.329;EFF=DOWNSTREAM(MODIFIER|||||DDX11L1|processed_transcript|NON_CODING|ENST00000456328||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655||1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|8|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|6|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|6|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|6|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|6|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|5|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|5|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|5|1),SPLICE_SITE_ACCEPTOR(HIGH|||||WASH7P|protein_coding|NON_CODING|ENST00000438504|6|1),SPLICE_SITE_ACCEPTOR(HIGH|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|6|1),SPLICE_SITE_ACCEPTOR(HIGH|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|6|1) GT:AD:DP:GQ:PL 0/0:250,0:70:99:0,169,3371 0/0:250,0:78:99:0,199,4105 0/0:250,0:70:99:0,187,3984 0/0:250,0:63:99:0,166,3406 0/0:243,0:89:99:0,262,5364 0/0:250,0:62:99:0,172,3575 0/0:250,0:79:99:0,223,4726 0/0:249,1:80:99:0,181,4749 0/0:234,1:85:99:0,241,5015 0/1:205,27:73:99:371,0,3406 0/1:225,16:74:99:318,0,3528 0/0:250,0:64:99:0,193,3988 1 17563 . G A 79.88 . AC=1;AF=0.042;AN=24;BaseQRankSum=3.375;DP=3000;DS;Dels=0.00;FS=9.603;HRun=0;HaplotypeScore=0.9909;InbreedingCoeff=-0.0518;MQ=30.15;MQ0=97;MQRankSum=-1.386;QD=0.32;ReadPosRankSum=-0.446;EFF=DOWNSTREAM(MODIFIER|||||DDX11L1|processed_transcript|NON_CODING|ENST00000456328||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655||1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|4|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|7|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|5|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|5|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|4|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|5|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|4|1) GT:AD:DP:GQ:PL 0/0:243,7:250:99:0,202,2559 0/0:246,4:250:99:0,187,2479 0/0:250,0:250:99:0,256,3232 0/0:249,1:250:99:0,239,3309 0/0:231,18:250:21.61:0,22,2802 0/0:248,2:250:99:0,214,2657 0/1:232,18:250:99:121,0,1801 0/0:249,1:250:99:0,263,3184 0/0:238,12:250:6.72:0,7,2591 0/0:250,0:250:99:0,343,3875 0/0:247,3:250:99:0,280,3428 0/0:250,0:250:99:0,301,3416 1 17697 . G C 255.3 . AC=4;AF=0.167;AN=24;BaseQRankSum=-1.815;DP=2999;DS;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=1.7379;InbreedingCoeff=-0.2256;MQ=15.66;MQ0=86;MQRankSum=2.999;QD=0.26;ReadPosRankSum=-2.160;EFF=DOWNSTREAM(MODIFIER|||||DDX11L1|processed_transcript|NON_CODING|ENST00000456328||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655||1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|4|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|7|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|4|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|4|1) GT:AD:DP:GQ:PL 0/1:214,36:250:99:132,0,595 0/0:249,1:250:78.22:0,78,967 0/0:248,1:250:81.24:0,81,1022 0/1:216,34:250:91.94:92,0,404 0/0:226,24:250:56.86:0,57,1099 0/0:245,4:249:23.87:0,24,704 0/0:225,25:250:2.97:0,3,746 0/1:216,33:250:80.80:81,0,810 0/0:245,4:250:73.97:0,74,1201 0/1:222,28:250:12.96:13,0,920 0/0:249,1:250:87.24:0,87,1000 0/0:182,66:250:8.40:0,8,703 1 17722 . A G 32.03 . AC=3;AF=0.125;AN=24;BaseQRankSum=0.923;DP=2937;DS;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=1.9343;InbreedingCoeff=-0.1033;MQ=14.33;MQ0=62;MQRankSum=-4.474;QD=0.04;ReadPosRankSum=0.750;EFF=DOWNSTREAM(MODIFIER|||||DDX11L1|processed_transcript|NON_CODING|ENST00000456328||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655||1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|4|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|7|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|4|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|4|1) GT:AD:DP:GQ:PL 0/0:247,3:250:51.15:0,51,628 0/0:250,0:250:60.18:0,60,746 0/0:250,0:250:54.17:0,54,685 0/0:249,1:250:54.15:0,54,644 0/0:233,0:233:81.25:0,81,1014 0/0:235,4:239:45.13:0,45,549 0/0:249,0:250:45.13:0,45,514 0/0:249,1:250:78.20:0,78,853 0/0:247,0:247:90.24:0,90,1012 0/1:227,17:244:0.06:0,0,670 0/1:214,11:225:4.62:5,0,542 0/1:236,13:249:71.41:71,0,448 1 17730 . C A 102.87 . AC=5;AF=0.208;AN=24;BaseQRankSum=-11.508;DP=2968;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.0610;InbreedingCoeff=-0.2498;MQ=13.12;MQ0=24;MQRankSum=-4.433;QD=0.08;ReadPosRankSum=1.952;EFF=DOWNSTREAM(MODIFIER|||||DDX11L1|processed_transcript|NON_CODING|ENST00000456328||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655||1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|4|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|4|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|4|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|6|1),SPLICE_SITE_ACCEPTOR(HIGH|||||WASH7P|protein_coding|NON_CODING|ENST00000430492|7|1) GT:AD:DP:GQ:PL 0/0:246,4:250:36.11:0,36,464 0/0:244,5:249:57.17:0,57,727 0/0:244,6:250:48.15:0,48,628 0/0:247,3:250:51.13:0,51,621 0/1:242,8:250:26.26:26,0,830 0/0:246,4:250:48.14:0,48,601 0/1:238,11:250:48.54:49,0,386 0/0:244,5:249:42.12:0,42,491 0/0:239,3:243:23.74:0,24,609 0/1:221,13:234:13.85:14,0,482 0/1:232,11:243:7:7,0,501 0/1:238,12:250:73.18:73,0,368 1 17746 . A G 607.7 . AC=8;AF=0.333;AN=24;BaseQRankSum=13.191;DP=2993;DS;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.4155;InbreedingCoeff=-0.5280;MQ=11.87;MQ0=5;MQRankSum=-4.672;QD=0.30;ReadPosRankSum=3.574;EFF=DOWNSTREAM(MODIFIER|||||DDX11L1|processed_transcript|NON_CODING|ENST00000456328||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655||1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|3|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|5|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|4|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|4|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|3|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|4|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|3|1) GT:AD:DP:GQ:PL 0/0:206,44:250:7.45:0,7,373 0/0:221,29:250:5.12:0,5,468 0/0:224,26:250:3.61:0,4,382 0/0:216,34:250:9.49:0,9,405 0/1:243,7:250:43.06:43,0,781 0/1:195,55:250:99:113,0,232 0/1:218,32:250:44.30:44,0,212 0/1:219,31:250:0.03:0,0,330 0/1:211,39:250:74.42:74,0,236 0/1:209,34:243:68.40:68,0,298 0/1:172,77:249:99:193,0,137 0/1:219,30:250:99:137,0,197