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Illumina / Pisces

Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
GNU General Public License v3.0
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Targeting with bed files #49

Open ben-sanders opened 4 years ago

ben-sanders commented 4 years ago

I'm using geminimulti and pisces on some targeted amplicon sequencing, but each run might contain a different mix of amplicons located around the genome so I can't easily use the chromosomes option to restrict analysis to target regions. Pisces has the --intervalpaths option, which I think does what I want, but is there any way (or plan to add a way) to target Gemini to specific regions using a bed file? It's by far the slowest part of my pipeline.

tamsen commented 4 years ago

hi Ben,

Thanks for using Pisces.

Yes, the intervalpaths or -i option will do what you want for Pisces Variant Caller. I dont think Gemini has such an option yet. Re Gemini, the best you could do is use some external program (samtools) to trim down your bams as much as you can ahead of time, and see if that helps.

Yes, it would be a good idea for a future feature..

thanks Tamsen