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Vt

180 bytes added, 21:48, 6 April 2017
Filters
This allows you to only analyse biallelic indels that are passed on chromosome 20.
vt profile_na12878 vt.bcf -g na12878.reference.txt -r genome.fa -f "N_ALLELE==2&&VTYPE==INDEL&&PASS" -i 20
 
This allows you to extract biallelic indels that are passed on chromosome 20.
vt view vt.bcf -g na12878.reference.txt -r genome.fa -f "N_ALLELE==2&&VTYPE==INDEL&&PASS" -i 20
Other examples of filters
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