Error while parsing vcf file

Question

[a.james]

Hello,

I am trying to convert my multiple vcf file into a tabular format. And I am having error while parsing through each row of the file here is part of the script,

 for files in results:
       Va_BM = vcf.Reader(filename=files, compressed=False) 
 for variant in Va_BM:
            tumor_REL        = variant.samples[0]
            normal_ID       = variant.samples[1]

The error, is ,

ValueError                                Traceback (most recent call last)
/home/usr/Tools/anaconda3/lib/python3.4/site-packages/vcf/parser.py in _parse_samples(self, samples, samp_fmt, site)
    464                         try:
--> 465                             sampdat[i] = int(vals)
    466                         except ValueError:

ValueError: invalid literal for int() with base 10: '86,2'

During handling of the above exception, another exception occurred:

ValueError                                Traceback (most recent call last)
<ipython-input-131-857e0813455d> in <module>()
      9 
     10     #  iterating lines in VCF file (one line = one variant)
---> 11     for variant in Va_BM:
     12         tumor_REL        = variant.samples[0]
     13         normal_ID       = variant.samples[1]

/home/usr/Tools/anaconda3/lib/python3.4/site-packages/vcf/parser.py in __next__(self)
    565 
    566         if fmt is not None:
--> 567             samples = self._parse_samples(row[9:], fmt, record)
    568             record.samples = samples
    569

Dont understand where I am going wrong, the vcf file is from Mutect2 and file format is ##fileformat=VCFv4.2 any help would be great. Thank you

[Pierre Lindenbaum]

search your VCF for the word '86,2' in the genotypes . There is a problem with your vcf at this point. Your parser expects an integer.

[a.james]

Thats the first line of my vcf file I mean after header, and I am wondering 82, 2 is in int format isnt?

[Pierre Lindenbaum]

why don't you show us the whole line ?????

[a.james]

Here is the whole line which complaints,

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  TUMOR   NORMAL

1   14748   .   G   C   .   alt_allele_in_normal;t_lod_fstar    ECNT=1;HCNT=4;MAX_ED=.;MIN_ED=.;NLOD=29.34;TLOD=4.58;CSQ=C|non_coding_transcript_exon_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|10/10||||1284|||||||-1||HGNC|38034|||||||||||||||||||||||||||||,C|non_coding_transcript_exon_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|12/12||||1398|||||||-1||HGNC|38034|||||||||||||||||||||||||||||,C|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1078|1||HGNC|37102|||||||||||||||||||||||||||||,C|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||339|1||HGNC|37102|||||||||||||||||||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene||10/10||||||||||-1||HGNC|38034|||||||||||||||||||||||||||||,C|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||336|1||HGNC|37102|||||||||||||||||||||||||||||,C|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||339|1||HGNC|37102|||||||||||||||||||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene||12/12||||||||||-1||HGNC|38034|||||||||||||||||||||||||||||,C|non_coding_transcript_exon_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|9/9||||1031|||||||-1||HGNC|38034|||||||||||||||||||||||||||||    GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1  0/1:`86,2`:0.027:1:1:0.500:2974,76:43:43  0/0:176,5:0.032:3:2:0.600:6048,155:92:84

[Pierre Lindenbaum]

you put the quote around 86,2 to highlight the number don't you ? or there are really some quotes in the VCF file (and it's the error)

[a.james]

No, I just highlighted it for bio-stars. There is no quote in real vcf file.

[a.james]

@Pierre Lindenbaum, apparently the issue is with vcf.reader parser doesn't suit for vcf 4.2 files.