Question: WGS tumor-only samples allele frequency
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gravatar for noemichael
2.9 years ago by
noemichael0
United States
noemichael0 wrote:

We have tumor-only WGS data...

I did allignment with the GATK pipeline. After that, I did variant calling with SamTools. This gives me a VCF file with in the INFO-column, the DP4 (giving me the amount of reads (both forward and reverse) with the reference sequence and the amount of reads (both forward and reverse) with the alternative sequence).

I wanted to make an allele frequency scatter, to search for large areas of CNA or LOH... However, CNVkit does not accept it like this. Is there an uncomplicated way to get a SNP-array / allele frequency scatter from WGS?

allele frequency genome • 835 views
ADD COMMENTlink modified 2.8 years ago by Biostar ♦♦ 20 • written 2.9 years ago by noemichael0
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