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bioinfo-pf-curie / TMB

Tumor Mutational Burden
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vcf file contains two sample #6

Open wangdepin opened 3 years ago

wangdepin commented 3 years ago

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 commented 3 years ago

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 commented 3 years ago

thank you so much!