search

andyrimmer / Platypus

Platypus Variant Caller
GNU General Public License v3.0
105 stars 38 forks source link

Filtering germline variants #87

Open dollinad opened 4 years ago

dollinad commented 4 years ago

Hi,

We have used Platypus to call somatic variants by using the following command on Linux - Centos7

python Platypus.py callVariants --genSNPs=1 --genIndels=0 -o path_to_output --refFile=hg38_no_alt.fa --bamFiles=tumor_bam,normal_bam --nCPU=5

The above command generates a vcf file with over 5 million variants which is much more than other tools we have tested using the same sample.

I was wondering if there is a way to only call somatic variants or flter the germline variants.

Thanks, Dollina