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bioinfo-pf-curie / TMB

Tumor Mutational Burden
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The format of input #4

Open deb0612 opened 3 years ago

deb0612 commented 3 years ago

Dear sir, I use mutect2 to call the somatic variants and use filtermutectcalls to generate the FILTER field. Finally, I use annovar to annotate the mutect2 output file and get three file(multianno.txt, multianno.vcf, .avinput) I use .multianno.vcf as pyTMB input. The error appeared below: image Which input file should I choose ? If I use the output of FilterMutectCalls and pyTMB goes well, but some arguments doesn't work.

tomgutman commented 3 years ago

Hello,

the multianno.vcf file is the one you should use to compute TMB score.

Apparently the multianno.vcf file is not recognize by pyTMB here. Are you sure the path to the file is the right one or the file exists ?