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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 8e20575721a463931a4b9fbbe905d90cc2863575"
author iuc
date Tue, 02 Mar 2021 17:46:39 +0000
parents 1fbe84e8a740
children
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##fileformat=VCFv4.1
##fileDate=.
##source=strelka
##source_version=2.9.10
##startTime=.
##cmdline=./configureStrelkaGermlineWorkflow.py --bam input_sample_0.bam --bam input_sample_1.bam --bam input_sample_2.bam --disableSequenceErrorEstimation --config=/tmp/tmpmywmzdlj/job_working_directory/000/7/configs/tmpzw3187cr --referenceFasta input_ref.fasta --runDir results
##reference=file:///tmp/tmpmywmzdlj/job_working_directory/000/7/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=79.00
##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">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12891
demo20	1	.	T	.	.	LowGQX	END=899;BLOCKAVG_min30p3a	GT:GQX:DP:DPF:MIN_DP	.:.:0:0:0
demo20	900	.	G	.	.	LowGQX;LowDepth	END=906;BLOCKAVG_min30p3a	GT:GQX:DP:DPF:MIN_DP	0/0:5:2:0:2
demo20	907	.	T	.	.	LowGQX	END=931;BLOCKAVG_min30p3a	GT:GQX:DP:DPF:MIN_DP	0/0:7:4:0:3
demo20	932	.	G	.	.	PASS	END=990;BLOCKAVG_min30p3a	GT:GQX:DP:DPF:MIN_DP	0/0:15:8:0:6
demo20	991	.	C	G	75	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
demo20	992	.	C	.	.	PASS	END=1084;BLOCKAVG_min30p3a	GT:GQX:DP:DPF:MIN_DP	0/0:24:14:0:9
demo20	1085	.	T	.	.	PASS	.	GT:GQX:DP:DPF:MIN_DP	0/0:22:21:1:21
demo20	1086	.	G	.	.	PASS	END=1148;BLOCKAVG_min30p3a	GT:GQX:DP:DPF:MIN_DP	0/0:54:22:1:19
demo20	1148	.	C	CTAT	144	PASS	CIGAR=1M3I;RU=TAT;REFREP=1;IDREP=2;MQ=59	GT:GQ:GQX:DPI:AD:ADF:ADR:FT:PL	0/1:114:27:20:11,8:5,3:6,5:PASS:111,0,147
demo20	1149	.	T	.	.	PASS	END=1270;BLOCKAVG_min30p3a	GT:GQX:DP:DPF:MIN_DP	0/0:39:19:0:14
demo20	1271	.	A	G	268	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
demo20	1272	.	G	.	.	PASS	END=1507;BLOCKAVG_min30p3a	GT:GQX:DP:DPF:MIN_DP	0/0:39:20:1:14
demo20	1508	.	A	G	312	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
demo20	1509	.	G	.	.	PASS	END=1582;BLOCKAVG_min30p3a	GT:GQX:DP:DPF:MIN_DP	0/0:27:17:0:10
demo20	1583	.	A	.	.	PASS	END=1669;BLOCKAVG_min30p3a	GT:GQX:DP:DPF:MIN_DP	0/0:21:15:0:8
demo20	1670	.	C	.	.	PASS	END=1705;BLOCKAVG_min30p3a	GT:GQX:DP:DPF:MIN_DP	0/0:45:19:0:16
demo20	1706	.	C	T	608	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
demo20	1707	.	G	.	.	PASS	END=1743;BLOCKAVG_min30p3a	GT:GQX:DP:DPF:MIN_DP	0/0:54:21:0:19
demo20	1744	.	C	T	312	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
demo20	1745	.	G	.	.	PASS	END=1845;BLOCKAVG_min30p3a	GT:GQX:DP:DPF:MIN_DP	0/0:40:21:1:16
demo20	1846	.	C	T	165	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
demo20	1847	.	G	.	.	PASS	END=1872;BLOCKAVG_min30p3a	GT:GQX:DP:DPF:MIN_DP	0/0:60:23:1:21
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
demo20	1874	.	C	.	.	PASS	END=2073;BLOCKAVG_min30p3a	GT:GQX:DP:DPF:MIN_DP	0/0:45:21:0:16
demo20	2074	.	T	C	246	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
demo20	2075	.	A	.	.	PASS	END=2198;BLOCKAVG_min30p3a	GT:GQX:DP:DPF:MIN_DP	0/0:63:31:1:22
demo20	2199	.	G	A	297	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
demo20	2200	.	C	.	.	PASS	END=2300;BLOCKAVG_min30p3a	GT:GQX:DP:DPF:MIN_DP	0/0:60:30:1:26
demo20	2301	.	G	T	369	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
demo20	2302	.	T	.	.	PASS	END=2454;BLOCKAVG_min30p3a	GT:GQX:DP:DPF:MIN_DP	0/0:72:30:0:25
demo20	2455	.	T	C	889	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
demo20	2456	.	G	.	.	PASS	END=2511;BLOCKAVG_min30p3a	GT:GQX:DP:DPF:MIN_DP	0/0:87:36:2:30
demo20	2512	.	A	G	531	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
demo20	2513	.	T	.	.	PASS	END=2639;BLOCKAVG_min30p3a	GT:GQX:DP:DPF:MIN_DP	0/0:81:37:1:28
demo20	2640	.	C	T	751	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
demo20	2641	.	T	.	.	PASS	END=2659;BLOCKAVG_min30p3a	GT:GQX:DP:DPF:MIN_DP	0/0:60:23:0:21
demo20	2660	.	G	T	567	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
demo20	2661	.	G	.	.	PASS	END=3037;BLOCKAVG_min30p3a	GT:GQX:DP:DPF:MIN_DP	0/0:41:27:1:18
demo20	3038	.	C	.	.	PASS	END=3053;BLOCKAVG_min30p3a	GT:GQX:DP:DPF:MIN_DP	0/0:27:20:1:17
demo20	3054	.	G	C	214	PASS	SNVHPOL=2;MQ=59	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
demo20	3055	.	C	.	.	PASS	END=3365;BLOCKAVG_min30p3a	GT:GQX:DP:DPF:MIN_DP	0/0:51:25:1:18
demo20	3366	.	G	T	753	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
demo20	3367	.	G	.	.	PASS	END=3536;BLOCKAVG_min30p3a	GT:GQX:DP:DPF:MIN_DP	0/0:60:28:0:21
demo20	3537	.	C	T	191	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
demo20	3538	.	T	.	.	PASS	END=3664;BLOCKAVG_min30p3a	GT:GQX:DP:DPF:MIN_DP	0/0:54:29:1:19
demo20	3664	.	TC	T	572	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
demo20	3665	.	C	.	.	PASS	.	GT:GQX:DP:DPF:MIN_DP	0:249:19:0:19
demo20	3666	.	C	.	.	PASS	END=4019;BLOCKAVG_min30p3a	GT:GQX:DP:DPF:MIN_DP	0/0:48:32:1:17
demo20	4020	.	C	.	.	PASS	END=4059;BLOCKAVG_min30p3a	GT:GQX:DP:DPF:MIN_DP	0/0:24:12:1:9
demo20	4060	.	C	.	.	PASS	END=4072;BLOCKAVG_min30p3a	GT:GQX:DP:DPF:MIN_DP	0/0:15:6:0:6
demo20	4073	.	C	.	.	LowGQX	END=4091;BLOCKAVG_min30p3a	GT:GQX:DP:DPF:MIN_DP	0/0:7:4:0:3
demo20	4092	.	T	.	.	LowGQX;LowDepth	END=4100;BLOCKAVG_min30p3a	GT:GQX:DP:DPF:MIN_DP	0/0:3:1:0:1
demo20	4101	.	T	.	.	LowGQX	END=5000;BLOCKAVG_min30p3a	GT:GQX:DP:DPF:MIN_DP	.:.:0:0:0