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mutation calling using bcftools or mutect #76

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crazyhottommy opened this issue Nov 9, 2017 · 0 comments

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commented Nov 9, 2017

Following a discussion here #37 and my zoom call with Erin.

I recently deal with SNV calling a lot and gained experience with various variant callers such as mutect (now part of GATK), freebayes (not a somatic caller) and lancet.
In real-life, do any one uses bcftools for variant calling? No matter what callers one uses, the downstream filtering is very important. So, what should we teach for the leaners?

should we teach mutect which can be used for a real-life data sets?

we can leave the development of the somatic calling after the first release.

Best,
Tommy

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