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, 21:50, 15 June 2014
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| | This discovery set appears to have many novel variants! (or false positives) | | This discovery set appears to have many novel variants! (or false positives) |
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| − | ==Peek==
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| − | You can see what you have in the file with:
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| − | vt peek mills.genotypes.bcf
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| − | You can also focus on a chromosome:
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| − | vt peek mills.genotypes.bcf -i 20
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| − | Or with just passed variants:
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| − | vt peek mills.genotypes.bcf -i 20 -f PASS
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| − | Or with failed variants:
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| − | vt peek mills.genotypes.bcf -i 20 -f ~PASS
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| − | Or with just 1bp indels:
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| − | vt peek mills.genotypes.bcf -i 20 -f "PASS&&DLEN==1"
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| − | Or with just 1bp deletions:
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| − | vt peek mills.genotypes.bcf -i 20 -f "PASS&&LEN==-1"
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| − | Or with just biallelic 1bp indels:
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| − | vt peek mills.genotypes.bcf -i 20 -f "PASS&&N_ALLELE==2&&LEN==1"
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| − | Or with just biallelic 1bp indels that are somewhat rare:
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| − | vt peek mills.sites.bcf -f "PASS&&N_ALLELE==2&&LEN==1&&INFO.AF<0.03"
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| − | Or with just biallelic 1bp indels that are somewhat rare with sanity checking:
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| − | vt peek mills.sites.bcf -f "PASS&&N_ALLELE==2&&LEN==1&&INFO.AC/INFO.AN<0.03"
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| − | which you will observe discrepancies due to rounding off in AF. So you should probably use INFO.AC/INFO.AN.
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| | ==Normalization== | | ==Normalization== |
