Mercurial > repos > iuc > bbtools_callvariants
diff test-data/cv_output.vcf @ 0:18b91d72794b draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
| author | iuc |
|---|---|
| date | Tue, 05 Oct 2021 20:05:50 +0000 |
| parents | |
| children | 7e041c120b96 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cv_output.vcf Tue Oct 05 20:05:50 2021 +0000 @@ -0,0 +1,60 @@ +##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