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AstraZeneca-NGS / VarDict

VarDict
MIT License
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Running on WGS samples #143

Closed vymao closed 4 years ago

vymao commented 4 years ago

Hi,

I am interested in running VarDict on WGS samples. I tried running it without a BED file for b37 but I get no variants called (I only see a VCF header). When I tried running VarDict on targeted panel sequencing with a BED file, it worked fine.

This was the command I used: 

AF_THR="0.01"

tumor_sample_name=$1
tumor_bam=$2
normal_sample_name=$3
normal_bam=$4

vardict -G /path/to/b37/human_g1k_v37_decoy.fasta -f $AF_THR -N ${tumor_sample_name}\
 -b "${tumor_bam}|${normal_bam}" | testsomatic.R | var2vcf_paired.pl -N\
 "${tumor_sample_name}|${normal_sample_name}" -f $AF_THR

Is a BED file necessary? If so, how can we get one for b37?

PolinaBevad commented 4 years ago

Hi Viktor, I answered to issue in VarDictJava repository, so I'll close this one!