List index out of range

Question

[Samiah]

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.

[pbpanigrahi]

Two quick things to check

• Header mismatch? What if u use ID in first column.
• Just check whether the columns are separated by same delimiter. It may happen that sample one is tab separated and urs is space separated. Just double check.

Let us know if u still see same error.

[Samiah]

Hey thank you pbpanigrahi, your answer solved my problem. The issue was header mismatch.

[pbpanigrahi]

Glad to hear it solved.

Please mark the above answer as resolved and also in this forum you should upvote when you find any suggestion helpful :)

[Arsenal]

Have you tried ANNOVAR? It is updated until this year.

[Samiah]

Thank you Arsenal, I will try it.