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samtools / bcftools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
http://samtools.github.io/bcftools/
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about GT’ calculation #1665

Closed yuanjianwen-gif closed 2 years ago

yuanjianwen-gif commented 2 years ago

I am using bcftools to call A to G transition in mRNA with RNAseq data， instead of snp at genomics ，and notice that there are mutations annotated 0/0 genotype but with high edited frequency (like DP4_alt = 50 , DP4_total = 200 ). It is really confusing what matters for genotype likehood calculation. Or it is not reasonable to use bctools to call mutation in mRNA

pd3 commented 2 years ago

The program bcftools call assumes diploid or haploid genotypes and is not intended for detection of somatic mutations / RNA editing. For that, I recommend running like this

bcftools mpileup -a AD ... | bcftools call -mA ...

ignoring GTs and postprocessing the output using a custom script based on AD depths. The mathematical model of call -mv (described here http://samtools.github.io/bcftools/call-m.pdf) cannot detect mosaic variants well.