Question: Input files for somaticSignature
0
gravatar for poojitha.ojamies
2.9 years ago by
poojitha.ojamies0 wrote:

Hello,

We use Varscan to make our somatic mutation calls. I would like to know if I can use the vcf files generated by Varscan for SomaticSignatures or i would need to redo the variant annotation with the variantannotator? Can I extract the relevant info from Varscan output instead?
 

 

somaticsignatures • 377 views
ADD COMMENTlink modified 2.9 years ago by Julian Gehring1.3k • written 2.9 years ago by poojitha.ojamies0
Answer: Input files for somaticSignature
0
gravatar for Julian Gehring
2.9 years ago by
Julian Gehring1.3k
Julian Gehring1.3k wrote:

A minimal VCF file will sufficient for the analysis, as long as it has the details for defining groups of interest (see the vignette which groups according to cancer type). So there should be no need to preprocess the data with variant annotator or other programs.

ADD COMMENTlink written 2.9 years ago by Julian Gehring1.3k
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