Mercurial > repos > iuc > bbtools_callvariants
comparison test-data/cv_output.vcf @ 10:7e041c120b96 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb
author | iuc |
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date | Tue, 27 Aug 2024 10:14:45 +0000 |
parents | 18b91d72794b |
children |
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9:66b138a2e74c | 10:7e041c120b96 |
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1 ##fileformat=VCFv4.2 | 1 ##fileformat=VCFv4.2 |
2 ##BBMapVersion= | 2 ##BBMapVersion=39.08 |
3 ##ploidy=2 | 3 ##ploidy=2 |
4 ##rarity=1.00000 | 4 ##rarity=1.00000 |
5 ##minallelefraction=0.10000 | 5 ##minallelefraction=0.10000 |
6 ##reads=2207 | 6 ##reads=2207 |
7 ##pairedReads=0 | 7 ##pairedReads=0 |
8 ##properlyPairedReads=0 | 8 ##properlyPairedReads=0 |
9 ##readLengthAvg= | 9 ##readLengthAvg=145.462 |
10 ##properPairRate=0.00000 | 10 ##properPairRate=0.00000 |
11 ##totalQualityAvg= | 11 ##totalQualityAvg=36.580 |
12 ##mapqAvg=43.348 | 12 ##mapqAvg=43.348 |
13 ##reference= | 13 ##reference=/home/bag/projects/code/tools-iuc/tools/bbtools/test-data/NC_002945v4.fasta |
14 ##contig=<ID=NC_002945.4,length=7000> | 14 ##contig=<ID=NC_002945.4,length=7000> |
15 ##FILTER=<ID=FAIL,Description="Fail"> | 15 ##FILTER=<ID=FAIL,Description="Fail"> |
16 ##FILTER=<ID=PASS,Description="Pass"> | 16 ##FILTER=<ID=PASS,Description="Pass"> |
17 ##INFO=<ID=SN,Number=1,Type=Integer,Description="Scaffold Number"> | 17 ##INFO=<ID=SN,Number=1,Type=Integer,Description="Scaffold Number"> |
18 ##INFO=<ID=STA,Number=1,Type=Integer,Description="Start"> | 18 ##INFO=<ID=STA,Number=1,Type=Integer,Description="Start"> |
51 ##FORMAT=<ID=NVC,Number=1,Type=Integer,Description="Nearby Variation Count"> | 51 ##FORMAT=<ID=NVC,Number=1,Type=Integer,Description="Nearby Variation Count"> |
52 ##FORMAT=<ID=FLG,Number=1,Type=Integer,Description="Flagged"> | 52 ##FORMAT=<ID=FLG,Number=1,Type=Integer,Description="Flagged"> |
53 ##FORMAT=<ID=SB,Number=1,Type=Float,Description="Strand Bias"> | 53 ##FORMAT=<ID=SB,Number=1,Type=Float,Description="Strand Bias"> |
54 ##FORMAT=<ID=SC,Number=1,Type=Float,Description="Score"> | 54 ##FORMAT=<ID=SC,Number=1,Type=Float,Description="Score"> |
55 ##FORMAT=<ID=PF,Number=1,Type=String,Description="Pass Filter"> | 55 ##FORMAT=<ID=PF,Number=1,Type=String,Description="Pass Filter"> |
56 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT | 56 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT dataset_4f1db038-76fe-46bc-a222-dfc4894a8ff2.dat |
57 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 | 57 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;RAF=1;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 1/1:2:2:1:1:0:0:0.9980:22.21:PASS |
58 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 | 58 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;RAF=1;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 1/1:2:2:1:1:0:0:0.9980:27.20:PASS |
59 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 | 59 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;RAF=1;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 1/1:2:2:1:1:0:0:0.9980:27.85:PASS |
60 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 | 60 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;RAF=1;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 GT:DP:AD:AF:RAF:NVC:FLG:SB:SC:PF 1/1:2:2:1:1:0:0:1:23.34:PASS |