checking many somatic mutations in IGV

Question

[pbu]

I need to check a few thousand somatic variants in IGV to remove the obvious false positives. Usually I open the germline and tumor bam files (exome sequencing) in IGV, generate a list of "regions of interest" based on the output of the variant caller, and start clicking through the list.

Does anyone have suggestions how to do this in a more efficient way without developing a mouse finger?

[User 59]

What possible reason can you have for examining each one by eye? This is impossible to do in genome scale experiments. So don't. If you have false positives then find some way of filtering them out based on some criteria in the VCF.

[Amitm]

hi,

If your criteria of false positives is Read depth, strand-bias or germline freq. then these all are present in the VCF file. Write a parser to pick out those values for each mut. OR, use vcftools, GATK utilities for Variant evaluation. You haven't mentioned what caller you used. Most somatic mut. callers have filters available for above such criteria.

Answer 1

[trausch]

You can execute a batch file with IGV and create one plot for every mutation

https://www.broadinstitute.org/igv/batch

However, screening a thousand plots doesn't appear particularly useful to me.