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bioinfo-pf-curie / TMB

Tumor Mutational Burden
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sys.stderr.write("Error: " + len(vcf.samples) #3

Open deb0612 opened 3 years ago

deb0612 commented 3 years ago

Dear sir, I use the command below: python bin/pyTMB.py -i WES-N0440vs5.gnomad.g1kpon.vcf --bed "/Everythings/bed/hg38/Roche_KAPA_HyperExome_hg38_capture_targets.bed" --dbConfig config/annovar --varConfig conf/mutect2.yml --polymDb 1k,gnomad > TMB_results.log and got the error

Traceback (most recent call last): File "bin/pyTMB.py", line 305, in sys.stderr.write("Error: " + len(vcf.samples) + TypeError: must be str, not int

The input vcf was generated from gatk 4.1.9 mutect2 reference genome: Homo_sapiens_assembly38.fasta

nservant commented 3 years ago

Hi, I made a quick fix. Please note that we shoul release a new version in the coming days. Best

deb0612 commented 3 years ago

Dear sir, I had tried the new version. It works well. But if I use mutect2 tumor-normal output as input of TMB.

$ python bin/pyTMB.py -i WES-N0440vs5.gnomad.g1kpon.vcf.hg38.filtered.vcf" --bed "/Everythings/bed/hg38/Roche_KAPA_HyperExome_hg38_capture_targets.bed" --dbConfig config/annovar_102015.yml --varConfig config/mutect2.yml --minDepth 100 --filterLowQual --filterNonCoding --filterSplice --filterSyn --filterPolym --polymDb 1k,gnomad --export >test.log

It showeda message: Error: 2 sample detected. This version is designed for a single sample !

Here is my input file look like: image

Is there any suggestion to delete another sample column?

nservant commented 3 years ago

you can try to use the --sample parameter with the name of the sample you would like to focus