An error is reported while running

[huilin-al]

python /home/kpadmin/biosoft/TMB/bin/pyTMB.py -i /home/kpadmin/TMB/LST_norm.vcf --effGenomeSize 33280000 --dbConfig /home/kpadmin/biosoft/TMB/config/snpeff.yml --varConfig /home/kpadmin/biosoft/TMB/config/mutect2.yml --vaf 0.05 --maf 0.001 --minDepth 20 --minAltDepth 2 --filterLowQual --filterNonCoding --filterSyn --filterPolym --polymDb 1k,gnomad > TMB_results.
error
Traceback (most recent call last):
File "/home/kpadmin/biosoft/TMB/bin/pyTMB.py", line 538, in
elif 0 <= args.vaf <= 1 and 0 <= min(freqs_vaf) <= 100 and max(freqs_vaf) > 1:
ValueError: min() arg is an empty sequence

Why and how to solve it

[tomgutman]

Hello,

Are you using the last version of the tool ?
The problem is related to the VAF column in your VCF file. Are the values comprised between 0 and 1 or between 0 and 100 ?

Best
Tom