d) Where do I find...?
Hi, I'm new to Variant Calling, and I am following the Somatic short variant discovery (SNVs + Indels) pipeline (https://gatk.broadinstitute.org/hc/en-us/articles/360035894731-Somatic-short-variant-discovery-SNVs-Indels-) with mouse data. So far, I have not encountered any trouble, though, according to GetpileupSummaries, the tool requires a common germline variant sites VCF, e.g. derived from the gnomAD resource, with population allele frequencies (AF) in the INFO field. I have acquired a dbSNP VCF from Sanger's Mouse Genomes Project for the FVB/N strain, GRCm38_68 assembly (ftp://ftp-mouse.sanger.ac.uk/current_snps/mgp.v5.merged.snps_all.dbSNP142.vcf.gz) but it does not contain the AF flag in the INFO field. Is there any way to add this requirement to the VCF?
Thanks in advance for your respose, I appreciate any support/guidance in the topic :) Have a nice day.
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