Entering edit mode
6.5 years ago
oghzzang
▴
50
How can I use PoN when running vardict?
I have PoN file and only tumor sample.
I want to run vardict with PoN.
How can I do that???
cf. vardict tumor only sample script
./vardict -G ~/ref/hg19.fasta -f 0.01 -N [Tumor sample] -b ./[Tumor bam] -c 1 -S 2 -E 3 -g 4 ./[tumor bed] | teststrandbias.R | var2vcf_valid.pl -N [Tumor sample] -E -f 0.01
