how to calculate TMB from call stats file
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10 months ago
rotemkat ▴ 10

Hi, I want calculate the TMB for each sample in a cohort i'm using. I have the mutations data in call stats file. I know that for the calculation i should know the number of non-synonymous somatic, coding, base substitution, per megabase of genome examined, but i'm not sure what data informs about the size of Mb?

Thanks in advance

mutations • 298 views
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You have to find out what kind of sequencing was done. Is it whole genome or exome? If exome, which panel was used?

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it was actually neither - this is RNA-seq data.

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You can use GATK CallableLoci to get the number of covered bases.

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