I ran cnvtogenes to annotate my varscan2 output. cnvtogenes is running fine on its test data but giving error on my sample data. The command I ran is:

sudo docker run -v ${PWD}:/data jeltje/cnvtogenes --cnvdir samples  -g hg38_annotation.bed > samples_annotation

where "samples" is directory containing varscan2 output files.

The Errorr I am getting is:

> final_m14 Traceback (most recent call last):   File
> "/usr/local/bin/cnvToGenes.py", line 136, in <module>
>     myseg = segment(inline.strip(), args.round)   File "/usr/local/bin/cnvToGenes.py", line 65, in __init__
>     self.chrom = cfields[1] IndexError: list index out of range

Below is the chunk of my sample file (final_m14.cnv) and cnvtogenes's test data (sample_1):

final_m14.cnv:

sample_1.cnv:

cnvtogenes was developed in 2016. I would be grateful if anyone could suggest me other latest and better tool for annotation of varscan2 output.

Thanks in advance.