Question: Varscan QUAL field
gravatar for megana.prasad
2.6 years ago by
megana.prasad0 wrote:


I am running Varscan through the galaxy interface. Although the tool runs correctly and generates a VCF file, the QUAL field is empty, i.e., has "." for each variant. I get this output both when running Varscan on an mpileup file and on individual pileup files. I wasn't able to find any settings regarding the QUAL field. Could you please tell me how to ensure that the QUAL score is calculated and reported?

Thanks, M

varscan • 773 views
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