Question: how to calculate TMB from call stats file
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gravatar for rotemkat
8 weeks ago by
rotemkat10
rotemkat10 wrote:

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 • 122 views
ADD COMMENTlink written 8 weeks ago by rotemkat10

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

ADD REPLYlink modified 8 weeks ago • written 8 weeks ago by igor12k

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

ADD REPLYlink written 7 weeks ago by rotemkat10

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

ADD REPLYlink written 7 weeks ago by igor12k
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