vcf file contains two sample

[wangdepin]

Dear Sir,
When I used the command below to calculate TMB, it happens to some error:
python ../../bin/pyTMB.py
-i ./629066_190229.snp_indel.filter.vcf
--effGenomeSize 33280000
--vaf 0.05 --maf 0.001 --minDepth 20 --minAltDepth 2
--filterLowQual --filterNonCoding --filterSyn --filterPolym
--polymDb 1k,gnomad
--dbConfig ../../config/annovar_102015.yml
--varConfig ../../config/mutect2.yml
Error: 2 sample detected. This version is designed for a single sample !
So, how to calculate TMB for vcf file which contains more sample? Thank you so much!

Depin.

[tomgutman]

Hello,

to compute TMB score from multisample vcf, you could specify the argument --sample with the sample ID to focus on on the command line.

Another more complex solution would be to split your vcf in mono-sample vcfs with
bcftools view -c1 -Oz -s $sample -o sample.vcf.gz multisample.vcf

Tom

[wangdepin]

thank you so much!