Vcf Files From 1000 Genomes For Pypgen

Question

[meganathan.pr]

I would like to use pypgen for my analyses. I have installed pypgen on my linux system and checked the installation with example VCF file which has resulted into expected output. Now I am trying to use the VCF files from 1000 genomes project but it gives following error message. Am I doing something wrong? Do I need to preprocess the VCF files from 1000 genomes project? Thanks.

Exception in thread Thread-2:
Traceback (most recent call last):
  File "/usr/lib/python2.7/threading.py", line 551, in __bootstrap_inner
    self.run()
  File "/usr/lib/python2.7/threading.py", line 504, in run
    self.__target(*self.__args, **self.__kwargs)
  File "/usr/lib/python2.7/multiprocessing/pool.py", line 314, in _handle_tasks
    for i, task in enumerate(taskseq):
  File "/usr/lib/python2.7/multiprocessing/pool.py", line 236, in <genexpr>
    self._taskqueue.put((((result._job, i, func, (x,), {})
  File "/home/Programs/pypgen-master/doc/src/package/scripts/vcfSNVfstats", line 52, in vcf_iterator
    vcf_line = parse_vcf_line(line, empty_vcf_line)
  File "/home/Programs/pypgen-master/doc/src/package/pypgen/parser/VCF.py", line 302, in parse_vcf_line
    genotype['GQ'] = float(genotype['GQ'])
KeyError: 'GQ'

[Sean Davis]

Does your VCF file contain a GQ format field? It appears that pypgen needs to access that field.

[Clare]

You are a step ahead of me, as I'm struggling to get the example vcf file to run. Could you share exactly how you ran the vcf. i.e. from what folder, and the commands. I typed the command vcfSNVfstats -i /home/pypgen-0.2.0/src/packages/scripts/example.vcf.gz -p pop1:c511,c512,c513,c514,c515,c563,c614,c630,c639,c640 pop2:pop2:m523,m524,m525,m589,m675,m676,m682,m683,m687,m689 -c 2 -r Chr01:1-10001 | head

I get the error vcfSNVfstats: command not found.
I'm sure I'm missing something really obvious here, any ideas?

[Sean Davis]

@Clare: Please ask another question rather than including your question in a comment. Feel free to include a link to this question in your new question if you think they are related.

Answer 1

[meganathan.pr]

@Sean Davis: Thanks for your reply. I have checked the VCF files from 1000 genomes. GQ field is missing in that data. Hope that is the problem. I found another tool vcftools which could do a similar jobs what I wish do. @Clare: You need to include backward slash '\' as given in the manual.

[Nick Crawford]

Pypgen author here. Sorry for the delay getting to this, but I defended my dissertation earlier this month and have been underwater. Anyway, pypgen is currently hard coded to expect a GQ field. I'll fix that in a future release.