Workflow for Variant Analysis

Question

[gkuffel22]

I have posted this question before and did not receive any responses. Let me try to articulate the issue more effectively this time. I have 200 samples (specifically from 200 different coyotes). I am trying to detect SNPs in the MHC gene. I have created a workflow in galaxy and would like to be able to use this to automate all of the steps required. At the end I would like all of the data to be compiled in one vcf file listed by sample name. The problem is I cannot find a way to have each sample maintain it's unique sample name through the workflow without manually entering this at some point. Any ideas?

[Ram]

1. Command line gives you more control than Galaxy does.
2. Ask on https://biostar.usegalaxy.org to reach the relevant audience.

[Devon Ryan]

You might want to check the internals of the GATK haplotype caller tool. It can accept multiple input BAM files, which is similar to what you need. The general idea is to accept a variable length argument and just replace the colnames() when producing the output (presuming you want to keep the results in the same file). As Ram said, you'd be best off asking on the galaxy site, they're a pretty helpful group.