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macarthur-lab / gnomad_browser

gnomAD browser pre-ASHG 2018
MIT License
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get_variants_from_sites_vcf crashes on sites with multiple alternate alleles #55

Closed ameynert closed 3 years ago

ameynert commented 7 years ago

Loading VCF files downloaded with gsutil to populate a local copy of gnomad. Errors like this:

Error parsing vcf line: 22 16157427 . G A,C 1640.05 PASS AC=3,1;AF=2.17707e-04,7.25689e-05;AN=13780;...;AC_Male=2,0;AC_Female=1,1; ..... Traceback (most recent call last): File "/array11/alison/gnomad/gnomad_browser/parsing.py", line 163, in get_variants_from_sites_vcf variant['ac_male'] = int(info_field['AC_Male']) ValueError: invalid literal for int() with base 10: '2,0'

Noticed in parsing.py line 147:

variant['allele_count'] = int(info_field['AC'].split(',')[i])

So I have modified lines 163-164:

variant['ac_male'] = int(info_field['AC_Male'].split(',')[i]) variant['ac_female'] = int(info_field['AC_Female'].split(',')[i])

This seems to have fixed the problem.

nawatts commented 6 years ago

https://github.com/macarthur-lab/gnomad_browser/pull/46 contains a fix for this.

nawatts commented 3 years ago

This repository is no longer being maintained. Development of the gnomAD browser has moved to broadinstitute/gnomad-browser.