annotate test-data/variants_test2.vcf @ 0:1fbe84e8a740 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"

##fileformat=VCFv4.1
##fileDate=.
##source=strelka
##source_version=2.9.10
##startTime=.
##cmdline=./configureStrelkaGermlineWorkflow.py --bam input_sample_0.cram --bam input_sample_1.cram --disableSequenceErrorEstimation --config=/tmp/tmpmxn8erma/job_working_directory/000/4/configs/tmpx1j1a_0u --referenceFasta input_ref.fasta --runDir results
##reference=file:///tmp/tmpmxn8erma/job_working_directory/000/4/working/input_ref.fasta
##contig=<ID=demo20,length=5000>
##content=strelka germline small-variant calls
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the region described in this record">
##INFO=<ID=BLOCKAVG_min30p3a,Number=0,Type=Flag,Description="Non-variant multi-site block. Non-variant blocks are defined independently for each sample. All sites in such a block are constrained to be non-variant, have the same filter value, and have sample values {GQX,DP,DPF} in range [x,y], y <= max(x+3,(x*1.3)).">
##INFO=<ID=SNVHPOL,Number=1,Type=Integer,Description="SNV contextual homopolymer length">
##INFO=<ID=CIGAR,Number=A,Type=String,Description="CIGAR alignment for each alternate indel allele">
##INFO=<ID=RU,Number=A,Type=String,Description="Smallest repeating sequence unit extended or contracted in the indel allele relative to the reference. RUs are not reported if longer than 20 bases">
##INFO=<ID=REFREP,Number=A,Type=Integer,Description="Number of times RU is repeated in reference">
##INFO=<ID=IDREP,Number=A,Type=Integer,Description="Number of times RU is repeated in indel allele">
##INFO=<ID=MQ,Number=1,Type=Integer,Description="RMS of mapping quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GQX,Number=1,Type=Integer,Description="Empirically calibrated genotype quality score for variant sites, otherwise minimum of {Genotype quality assuming variant position,Genotype quality assuming non-variant position}">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Filtered basecall depth used for site genotyping. In a non-variant multi-site block this value represents the average of all sites in the block.">
##FORMAT=<ID=DPF,Number=1,Type=Integer,Description="Basecalls filtered from input prior to site genotyping. In a non-variant multi-site block this value represents the average of all sites in the block.">
##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum filtered basecall depth used for site genotyping within a non-variant multi-site block">
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed. For indels this value only includes reads which confidently support each allele (posterior prob 0.51 or higher that read contains indicated allele vs all other intersecting indel alleles)">
##FORMAT=<ID=ADF,Number=.,Type=Integer,Description="Allelic depths on the forward strand">
##FORMAT=<ID=ADR,Number=.,Type=Integer,Description="Allelic depths on the reverse strand">
##FORMAT=<ID=FT,Number=1,Type=String,Description="Sample filter, 'PASS' indicates that all filters have passed for this sample">
##FORMAT=<ID=DPI,Number=1,Type=Integer,Description="Read depth associated with indel, taken from the site preceding the indel">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phase set identifier">
##FORMAT=<ID=SB,Number=1,Type=Float,Description="Sample site strand bias">
##FILTER=<ID=IndelConflict,Description="Indel genotypes from two or more loci conflict in at least one sample">
##FILTER=<ID=SiteConflict,Description="Site is filtered due to an overlapping indel call filter">
##FILTER=<ID=LowGQX,Description="Locus GQX is below threshold or not present">
##FILTER=<ID=HighDPFRatio,Description="The fraction of basecalls filtered out at a site is greater than 0.4">
##FILTER=<ID=HighSNVSB,Description="Sample SNV strand bias value (SB) exceeds 10">
##FILTER=<ID=HighDepth,Description="Locus depth is greater than 3x the mean chromosome depth">
##Depth_demo20=53.00
##FILTER=<ID=LowDepth,Description="Locus depth is below 3">
##FILTER=<ID=NotGenotyped,Description="Locus contains forcedGT input alleles which could not be genotyped">
##FILTER=<ID=PloidyConflict,Description="Genotype call from variant caller not consistent with chromosome ploidy">
##FILTER=<ID=NoPassedVariantGTs,Description="No samples at this locus pass all sample filters and have a variant genotype">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12891	NA12892
demo20	991	.	C	G	38	PASS	SNVHPOL=2;MQ=59	GT:GQ:GQX:DP:DPF:AD:ADF:ADR:SB:FT:PL	0/1:71:9:9:1:5,4:1,4:4,0:2.8:PASS:72,0,123	0/0:33:33:12:0:12,0:9,0:3,0:0.0:PASS:0,36,258
demo20	1148	.	C	CTAT	72	PASS	CIGAR=1M3I;RU=TAT;REFREP=1;IDREP=2;MQ=60	GT:GQ:GQX:DPI:AD:ADF:ADR:FT:PL	0/1:114:27:20:11,8:5,3:6,5:PASS:111,0,147	0/0:69:69:28:24,0:12,0:12,0:PASS:0,72,443
demo20	1271	.	A	G	134	PASS	SNVHPOL=4;MQ=60	GT:GQ:GQX:DP:DPF:AD:ADF:ADR:SB:FT:PL	0/1:126:30:18:0:8,10:7,6:1,4:-18.6:PASS:169,0,123	0/0:75:75:26:0:26,0:18,0:8,0:0.0:PASS:0,78,370
demo20	1508	.	A	G	156	PASS	SNVHPOL=3;MQ=60	GT:GQ:GQX:DP:DPF:AD:ADF:ADR:SB:FT:PL	0/1:172:30:22:1:10,12:4,6:6,6:-21.5:PASS:191,0,169	0/0:108:108:37:2:37,0:19,0:18,0:0.0:PASS:0,111,370
demo20	1706	.	C	T	304	PASS	SNVHPOL=2;MQ=59	GT:GQ:GQX:DP:DPF:AD:ADF:ADR:SB:FT:PL	1/1:54:30:19:0:0,19:0,8:0,11:-35.5:PASS:342,57,0	0/0:90:90:31:2:31,0:7,0:24,0:0.0:PASS:0,93,370
demo20	1744	.	C	T	156	PASS	SNVHPOL=3;MQ=59	GT:GQ:GQX:DP:DPF:AD:ADF:ADR:SB:FT:PL	0/1:159:30:21:0:9,12:5,6:4,6:-20.7:PASS:191,0,156	0/0:78:78:27:0:27,0:6,0:21,0:0.0:PASS:0,81,370
demo20	1846	.	C	T	83	PASS	SNVHPOL=3;MQ=60	GT:GQ:GQX:DP:DPF:AD:ADF:ADR:SB:FT:PL	0/1:116:30:24:1:16,8:13,5:3,3:-12.4:PASS:117,0,224	0/0:60:60:21:0:21,0:14,0:7,0:0.0:PASS:0,63,370
demo20	1873	.	C	T	122	PASS	SNVHPOL=3;MQ=60	GT:GQ:GQX:DP:DPF:AD:ADF:ADR:SB:FT:PL	0/0:60:60:21:0:21,0:15,0:6,0:0.0:PASS:0,63,360	0/1:155:30:23:0:13,10:8,7:5,3:-14.9:PASS:157,0,195
demo20	2074	.	T	C	123	PASS	SNVHPOL=2;MQ=60	GT:GQ:GQX:DP:DPF:AD:ADF:ADR:SB:FT:PL	0/1:156:30:24:1:13,11:4,8:9,3:-9.7:PASS:158,0,191	0/0:75:75:26:0:26,0:14,0:12,0:0.0:PASS:0,78,370
demo20	2199	.	G	A	149	PASS	SNVHPOL=3;MQ=60	GT:GQ:GQX:DP:DPF:AD:ADF:ADR:SB:FT:PL	0/1:181:30:28:1:14,14:12,5:2,9:-14.3:PASS:183,0,189	0/0:96:96:33:0:33,0:17,0:16,0:0.0:PASS:0,99,370
demo20	2301	.	G	T	184	PASS	SNVHPOL=2;MQ=59	GT:GQ:GQX:DP:DPF:AD:ADF:ADR:SB:FT:PL	0/1:161:22:29:1:12,17:6,11:6,6:-21.0:PASS:219,0,158	0/0:75:75:26:1:26,0:15,0:11,0:0.0:PASS:0,78,370
demo20	2455	.	T	C	445	PASS	SNVHPOL=2;MQ=60	GT:GQ:GQX:DP:DPF:AD:ADF:ADR:SB:FT:PL	1/1:90:30:31:2:0,31:0,14:0,17:-51.4:PASS:370,93,0	0/0:78:78:27:1:27,0:11,0:16,0:0.0:PASS:0,81,370
demo20	2512	.	A	G	266	PASS	SNVHPOL=2;MQ=59	GT:GQ:GQX:DP:DPF:AD:ADF:ADR:SB:FT:PL	0/1:151:22:39:1:13,26:9,11:4,15:-28.4:PASS:300,0,148	0/0:69:69:24:2:24,0:8,0:16,0:0.0:PASS:0,72,370
demo20	2640	.	C	T	375	PASS	SNVHPOL=3;MQ=60	GT:GQ:GQX:DP:DPF:AD:ADF:ADR:SB:FT:PL	1/1:81:30:28:0:0,28:0,14:0,14:-47.3:PASS:370,84,0	0/0:102:102:35:0:35,0:17,0:18,0:0.0:PASS:0,105,370
demo20	2660	.	G	T	283	PASS	SNVHPOL=3;MQ=60	GT:GQ:GQX:DP:DPF:AD:ADF:ADR:SB:FT:PL	1/1:60:30:21:1:0,21:0,11:0,10:-36.2:PASS:321,63,0	0/0:87:87:30:0:30,0:15,0:15,0:0.0:PASS:0,90,370
demo20	3054	.	G	C	107	PASS	SNVHPOL=2;MQ=58	GT:GQ:GQX:DP:DPF:AD:ADF:ADR:SB:FT:PL	0/1:140:22:20:0:10,10:6,6:4,4:-12.8:PASS:142,0,153	0/0:24:24:9:2:9,0:4,0:5,0:0.0:PASS:0,27,201
demo20	3366	.	G	T	377	PASS	SNVHPOL=4;MQ=60	GT:GQ:GQX:DP:DPF:AD:ADF:ADR:SB:FT:PL	1/1:75:30:26:0:0,26:0,15:0,11:-42.1:PASS:370,78,0	0/0:75:75:26:0:26,0:13,0:13,0:0.0:PASS:0,78,370
demo20	3537	.	C	T	95	PASS	SNVHPOL=2;MQ=59	GT:GQ:GQX:DP:DPF:AD:ADF:ADR:SB:FT:PL	0/1:128:22:31:1:21,10:8,6:13,4:-11.3:PASS:130,0,256	0/0:84:84:29:1:29,0:10,0:19,0:0.0:PASS:0,87,370
demo20	3664	.	TC	T	286	PASS	CIGAR=1M1D;RU=C;REFREP=4;IDREP=3;MQ=59	GT:GQ:GQX:DPI:AD:ADF:ADR:FT:PL	0/1:249:27:41:18,20:10,10:8,10:PASS:322,0,246	0/0:70:70:25:25,0:10,0:15,0:PASS:0,73,493