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Old 01-30-2014, 08:39 PM   #1
bylemcsmith
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Location: St. Lous

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Default SNP Filtering

I have a list of SNPs and I was wondering if I could get a response as to the best way to filter these SNPs. I would normally do it be Quality but I'm confused as to why some of the SNPs say VarscanHighConfidence but don't have a quality score.

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT TCGA-17-Z012-01A-01W-0746-08 TCGA-17-Z012-01A-01W-0746-08-Samtools TCGA-17-Z012-11A-01W-0746-08 TCGA-17-Z012-11A-01W-0746-08-Sniper TCGA-17-Z012-01A-01W-0746-08-Sniper TCGA-17-Z012-11A-01W-0746-08-VarscanSomatic TCGA-17-Z012-01A-01W-0746-08-VarscanSomatic TCGA-17-Z012-11A-01W-0746-08-Strelka TCGA-17-Z012-01A-01W-0746-08-Strelka
1 14907 . A G 8 . . GT:GQP:BQ:MQ:AD:FA:VAQ:SS:FT 0/1:8:7:34,35:22:4,3:0.429:8:.:IntersectionFailure-SnpFilter 0/1:8:7:34,35:22:4,3:0.429:8:.:SnpFilter .:.:.:.:.:.:.:.:.:. .:.:.:.:.:.:.:.:.:. .:.:.:.:.:.:.:.:.:. .:.:.:.:.:.:.:.:.:. .:.:.:.:.:.:.:.:.:. .:.:.:.:.:.:.:.:.:. .:.:.:.:.:.:.:.:.:.
1 14930 . A G . . . GTPP4:BQ:FA:VAQ:SS:FT:IGT:BCOUNT:GQ:JGQ:MQ:AMQ:SSC:AD 0/1:8:2,2,3,1:33,31:0.5:38:2:IntersectionFailure-SnpFilter:0/1:4,0,4,0:38:.:24:23,24:34:4,4 0/1:8:.,.,.,.:33,31:0.5:38:.:IntersectionFailure-SnpFilter:.:.,.,.,.:38:.:24:.:.:4,4 0/0:4:4,0,0,0:34:0:0:0:FalsePositive-IntersectionFailure:0/0:4,0,0,0:39:.:23:23:.:. 0/0:4:4,0,0,0:34:.:0:0:FalsePositive-IntersectionFailure:0/0:4,0,0,0:39:.:23:23:.:. 0/1:8:2,2,3,1:34,31:.:38:2:FalsePositive-IntersectionFailure:0/1:4,0,4,0:35:.:24:23,24:34:. 0/0:4:.,.,.,.:.:0:.:.:VarscanHighConfidence:.:.,.,.,.:.:.:.:.:.:. 0/1:8:2,2,3,1:.:0.5:8:2:VarscanHighConfidence:.:.,.,.,.:.:.:.:.:.:. .:.:.,.,.,.:.:.:.:.:.:.:.,.,.,.:.:.:.:.:.:. .:.:.,.,.,.:.:.:.:.:.:.:.,.,.,.:.:.:.:.:.:.
1 16257 . G C . . . GT:IGTPP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC:FT:AD:FA 0/1:0/1:5:1,1,1,1:0,2,2,0:18:.:18:34,31:25:30,23:2:18:IntersectionFailure-SnpFilter:3,2:0.4 0/1:.:5:.,.,.,.:.,.,.,.:18:.:18:34,31:25:.:.:.:IntersectionFailure-SnpFilter:3,2:0.4 0/0:0/0:1:1,0,0,0:0,0,1,0:15:.:0:36:15:15:0:.:FalsePositive-IntersectionFailure:.:. 0/0:0/0:1:1,0,0,0:0,0,1,0:15:.:0:36:15:15:0:.:FalsePositive-IntersectionFailure:.:. 0/1:0/1:4:1,1,1,1:0,2,2,0:8:.:21:31,34:27:30,23:2:18:FalsePositive-IntersectionFailure:.:. .:.:.:.,.,.,.:.,.,.,.:.:.:.:.:.:.:.:.:.:.:. .:.:.:.,.,.,.:.,.,.,.:.:.:.:.:.:.:.:.:.:.:. .:.:.:.,.,.,.:.,.,.,.:.:.:.:.:.:.:.:.:.:.:. .:.:.:.,.,.,.:.,.,.,.:.:.:.:.:.:.:.:.:.:.:.
1 30923 . G T 6 . . GT:GQP:BQ:MQ:AD:FA:VAQ:SS:FT 0/1:0:1:0,36:37:0,1:1:6:.:IntersectionFailure-SnpFilter 0/1:0:1:0,36:37:0,1:1:6:.:SnpFilter .:.:.:.:.:.:.:.:.:. .:.:.:.:.:.:.:.:.:. .:.:.:.:.:.:.:.:.:. .:.:.:.:.:.:.:.:.:. .:.:.:.:.:.:.:.:.:. .:.:.:.:.:.:.:.:.:. .:.:.:.:.:.:.:.:.:.
1 52238 . T G 31 . . GT:GQP:BQ:MQ:AD:FA:VAQ:SS:FT 1/1:3:2:0,31:33:0,2:1:31:.:IntersectionFailure-SnpFilter 1/1:3:2:0,31:33:0,2:1:31:.:SnpFilter .:.:.:.:.:.:.:.:.:. .:.:.:.:.:.:.:.:.:. .:.:.:.:.:.:.:.:.:. .:.:.:.:.:.:.:.:.:. .:.:.:.:.:.:.:.:.:. .:.:.:.:.:.:.:.:.:. .:.:.:.:.:.:.:.:.:.
1 55085 . T A . . . GTPP4:BQ:FA:VAQ:SS:FT:GQ:MQ:AD 1/1:4:0,0,2,1:0,33:1:42:1:IntersectionFailure-SnpFilter:9:20:0,4 1/1:4:.,.,.,.:0,33:1:42:.:SnpFilter:9:20:0,4 1/1:5:.,.,.,.:.:1:.:.:VarscanHighConfidence:.:.:. .:.:.,.,.,.:.:.:.:.:.:.:.:. .:.:.,.,.,.:.:.:.:.:.:.:.:. 1/1:5:.,.,.,.:.:1:.:.:VarscanHighConfidence:.:.:. 1/1:3:0,0,2,1:.:1:0:1:VarscanHighConfidence:.:.:. .:.:.,.,.,.:.:.:.:.:.:.:.:. .:.:.,.,.,.:.:.:.:.:.:.:.:.
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Old 01-31-2014, 06:13 AM   #2
chrisamiller
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VarscanHighConfidence is in the FT field. That's the name of the filter that removed that site (it failed the filter that retains high-confidence SNPs).
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