Mity merge - IndexError: list index out of range

[anjalijain22]

Hi,
I'm running into the below IndexError with mity merge:

mity 0.3.0
mity vcf merge
Traceback (most recent call last):
File "/home/ajain/.local/bin/mity", line 29, in
args.func(args)
File "/home/ajain/.local/lib/python3.9/site-packages/mitylib/commands.py", line 191, in _cmd_merge
merge.do_merge(args.mity_vcf, args.nuclear_vcf, args.prefix, genome)
File "/home/ajain/.local/lib/python3.9/site-packages/mitylib/merge.py", line 139, in do_merge
mity_number = mity_line.split("Number=")[1]
IndexError: list index out of range

The command I'm using is - mity merge --prefix combined --mity_vcf file.mity.vcf.gz --nuclear_vcf file_nuclear.vcf.gz in which the file.mity.vcf.gz file was generated using the mity call function.

I'd really appreciate your help on how to resolve this error. Thanks in advance!

[drmjc]

Hi, what nuclear variant caller did you use? I think it's failing on a line that's specific for GATK HaplotypeCaller. Thanks

[anjalijain22]

Thanks for your reply!
Yes, I used the GATK HaplotypeCaller. What would be the workaround for this error?

[drmjc]

Hi, It looks like the format of mity_line is unexpected. Can you share both vcf files? I only need the header lines and a small number of variants. Thanks

…

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[anjalijain22]

Sure, here are the nuclear and mity vcf files -
sample_mity.vcf.gz
sample_nuclear.vcf.gz

[drmjc]

Hi @anjalijain22,
thanks, but these vcf files are malformed, with aberrant " throughout - you'll see what i mean when you open them. I've spent a good while trying to fix them, but i get a different error relating to unicode that makes me think there's something wrong with the files. I'm gonna give up on these for now. perhaps try to deidentify them via a regex using a pipe rather than an editor.