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Revision as of 11:25, 10 December 2014
, 11:25, 10 December 2014→Looking at final INDEL VCF
$GC/bin/vt peek ~/$SAMPLE/output/indel/final/all.genotypes.vcf.gz
$GC/bin/vt peek ~/$SAMPLE/output/indel/final/all.genotypes.vcf.gz
no. Indels : 588566
no. Indels : 588566
2 alleles (ins/del) : 588566 (0.87) [273261/315305]
2 alleles (ins/del) : 588566 (0.87) [273261/315305]
Note that AB>0.5 denotes reference bias and AB<0.5 denotes alternative allele bias.
Note that AB>0.5 denotes reference bias and AB<0.5 denotes alternative allele bias.
$GC/bin/vt peek ~/$SAMPLE/output/indel/final/all.genotypes.vcf.gz -f "PASS&&INFO.AC>0&&INFO.AB<0.7&&INFO.AB>0.3"
$GC/bin/vt peek ~/$SAMPLE/output/indel/final/all.genotypes.vcf.gz -f "PASS&&INFO.AC>0&&INFO.AB<0.7&&INFO.AB>0.3"
no. Indels : 490965
no. Indels : 490965
2 alleles (ins/del) : 490965 (0.92) [235254/255711]
2 alleles (ins/del) : 490965 (0.92) [235254/255711]
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== Friday: Reviewing SNPCALL Results ==
== Friday: Reviewing SNPCALL Results ==
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