annotate test-data/util/build-data/test.comp_het.vcf @ 7:345d41f3f574 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"

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##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