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view test-data/cv_output.vcf @ 0:fc029a9b4d07 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
author iuc
date Mon, 06 Feb 2023 18:06:47 +0000
parents
children cab19c0452c4
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##fileformat=VCFv4.2
##BBMapVersion=
##ploidy=2
##rarity=1.00000
##minallelefraction=0.10000
##reads=2207
##pairedReads=0
##properlyPairedReads=0
##readLengthAvg=
##properPairRate=0.00000
##totalQualityAvg=
##mapqAvg=43.348
##reference=
##contig=<ID=NC_002945.4,length=7000>
##FILTER=<ID=FAIL,Description="Fail">
##FILTER=<ID=PASS,Description="Pass">
##INFO=<ID=SN,Number=1,Type=Integer,Description="Scaffold Number">
##INFO=<ID=STA,Number=1,Type=Integer,Description="Start">
##INFO=<ID=STO,Number=1,Type=Integer,Description="Stop">
##INFO=<ID=TYP,Number=1,Type=String,Description="Type">
##INFO=<ID=R1P,Number=1,Type=Integer,Description="Read1 Plus Count">
##INFO=<ID=R1M,Number=1,Type=Integer,Description="Read1 Minus Count">
##INFO=<ID=R2P,Number=1,Type=Integer,Description="Read2 Plus Count">
##INFO=<ID=R2M,Number=1,Type=Integer,Description="Read2 Minus Count">
##INFO=<ID=AD,Number=1,Type=Integer,Description="Allele Depth">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=MCOV,Number=1,Type=Integer,Description="Minus Coverage">
##INFO=<ID=PPC,Number=1,Type=Integer,Description="Paired Count">
##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Fraction">
##INFO=<ID=RAF,Number=1,Type=Float,Description="Revised Allele Fraction">
##INFO=<ID=LS,Number=1,Type=Integer,Description="Length Sum">
##INFO=<ID=MQS,Number=1,Type=Integer,Description="MAPQ Sum">
##INFO=<ID=MQM,Number=1,Type=Integer,Description="MAPQ Max">
##INFO=<ID=BQS,Number=1,Type=Integer,Description="Base Quality Sum">
##INFO=<ID=BQM,Number=1,Type=Integer,Description="Base Quality Max">
##INFO=<ID=EDS,Number=1,Type=Integer,Description="End Distance Sum">
##INFO=<ID=EDM,Number=1,Type=Integer,Description="End Distance Max">
##INFO=<ID=IDS,Number=1,Type=Integer,Description="Identity Sum">
##INFO=<ID=IDM,Number=1,Type=Integer,Description="Identity Max">
##INFO=<ID=NVC,Number=1,Type=Integer,Description="Nearby Variation Count">
##INFO=<ID=FLG,Number=1,Type=Integer,Description="Flagged">
##INFO=<ID=CED,Number=1,Type=Integer,Description="Contig End Distance">
##INFO=<ID=HMP,Number=1,Type=Integer,Description="Homopolymer Count">
##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
##INFO=<ID=DP4,Number=4,Type=Integer,Description="Ref+, Ref-, Alt+, Alt-">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Allele Depth">
##FORMAT=<ID=AF,Number=1,Type=Float,Description="Allele Fraction">
##FORMAT=<ID=RAF,Number=1,Type=Float,Description="Revised Allele Fraction">
##FORMAT=<ID=NVC,Number=1,Type=Integer,Description="Nearby Variation Count">
##FORMAT=<ID=FLG,Number=1,Type=Integer,Description="Flagged">
##FORMAT=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
##FORMAT=<ID=SC,Number=1,Type=Float,Description="Score">
##FORMAT=<ID=PF,Number=1,Type=String,Description="Pass Filter">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	
NC_002945.4	976327	.	N	T	22.21	PASS	SN=0;STA=976326;STO=976327;TYP=SUB;R1P=2;R1M=0;R2P=0;R2M=0;AD=2;DP=2;MCOV=-1;PPC=0;AF=1.0000;RAF=1.0000;LS=292;MQS=77;MQM=40;BQS=48;BQM=24;EDS=111;EDM=65;IDS=1930;IDM=972;NVC=0;FLG=0;CED=0;HMP=0;SB=0.9980	GT:DP:AD:AF:RAF:NVC:FLG:SB:SC:PF	1/1:2:2:1.0000:1.0000:0:0:0.9980:22.21:PASS
NC_002945.4	1501932	.	N	C	27.20	PASS	SN=0;STA=1501931;STO=1501932;TYP=SUB;R1P=0;R1M=2;R2P=0;R2M=0;AD=2;DP=2;MCOV=-1;PPC=0;AF=1.0000;RAF=1.0000;LS=292;MQS=88;MQM=44;BQS=64;BQM=39;EDS=74;EDM=38;IDS=1986;IDM=993;NVC=0;FLG=0;CED=0;HMP=0;SB=0.9980	GT:DP:AD:AF:RAF:NVC:FLG:SB:SC:PF	1/1:2:2:1.0000:1.0000:0:0:0.9980:27.20:PASS
NC_002945.4	3380579	.	N	G	27.85	PASS	SN=0;STA=3380578;STO=3380579;TYP=SUB;R1P=0;R1M=2;R2P=0;R2M=0;AD=2;DP=2;MCOV=-1;PPC=0;AF=1.0000;RAF=1.0000;LS=289;MQS=87;MQM=44;BQS=75;BQM=38;EDS=105;EDM=63;IDS=1986;IDM=993;NVC=0;FLG=0;CED=0;HMP=0;SB=0.9980	GT:DP:AD:AF:RAF:NVC:FLG:SB:SC:PF	1/1:2:2:1.0000:1.0000:0:0:0.9980:27.85:PASS
NC_002945.4	3646293	.	N	A	23.34	PASS	SN=0;STA=3646292;STO=3646293;TYP=SUB;R1P=1;R1M=1;R2P=0;R2M=0;AD=2;DP=2;MCOV=-1;PPC=0;AF=1.0000;RAF=1.0000;LS=291;MQS=86;MQM=44;BQS=76;BQM=38;EDS=44;EDM=31;IDS=1986;IDM=993;NVC=0;FLG=0;CED=0;HMP=0;SB=1.0000	GT:DP:AD:AF:RAF:NVC:FLG:SB:SC:PF	1/1:2:2:1.0000:1.0000:0:0:1.0000:23.34:PASS