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Old 06-11-2012, 03:21 AM   #1
genomicist
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Location: Sweden

Join Date: Jan 2011
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Default how does varscan somatic compute variant allele frequency?

Dear all,

I wonder how "varscan somatic" computes the variant allele frequencies. Is it by simple counting the reference bases (".", ",") and variant bases in the tumor pileup file and dividing the read count for the variant by the sum? Is there any filtering of the bases involved, e.g. by base quality or read mapping quality? In the publication (Koboldt et al, Genome Research 2012), it is stated that varscan requires minimum phred base quality of 20. Is it being used for calling the variant as well as calculating allele frequency?

Thanks in advance for your reply.
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