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bioinfo-pf-curie / TMB

Tumor Mutational Burden
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An error is reported while running #15

Open huilin-al opened 1 year ago

huilin-al commented 1 year ago

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 commented 1 year ago

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