mpileup 10 column format for copyCat

Question

[stephanie.hilz]

I am having a difficult time generating the 10-column mpileup file used as input for copyCat (I've downloaded an older version of samtools, samtools-0.1.16, and tried running mpileup with a variety of options, but had no luck). I am only able to get the 6-column format. I was wondering if anyone who has used copyCat would be able to share the samtools mpileup command they typically use to generate those files, as well as a few lines from an example file so that I can know what I am aiming for. I'd really appreciate it!

Answer 1

[hongen.hugo.xu]

mpileup 10 columns seems deprecated, see https://software.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_qc_CheckPileup.php

CopyCat also accepts VCF input, you may try this format. I am also trying to run CopyCat using VCF files as input.