sys.stderr.write("Error: " + len(vcf.samples)

[deb0612]

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]

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

[deb0612]

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:

Is there any suggestion to delete another sample column?

[nservant]

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