samtools mpileup with minimal filters
Hi,
I am running samtools mpileup (v1.4) on a bam file with very choppy coverage. I want to get a first-pass list of positions with SNVs and their frequency as reported by the read counts, but no matter what I do, I keep getting all SNVs filtered out as not passing QC.
What's the magic parameter set for an initial list of SNVs and frequencies?
Thanks
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