How do I extract GT information from VCF using PyVCF?

Question

[inkprs]

Hi,

Can you show an example to extract GT fields from below data (columns starting from 9th position included) using PyVCF?

FORMAT                  MATERIAL_A      MATERIAL_B      MATERIAL_C        MATERIAL_C

GT:DP:AR:AQ:AMXQ        ./.:0:0:.:.     1/1:1:1:31:31   1/0:4:2:30:31     ./.:0:0:.:.

[Santosh Anand]

Don't know python solution. But its easy to do by vcftools --extract-FORMAT-info <string>. See https://vcftools.github.io/man_latest.html

[WouterDeCoster]

Please choose sensible tags, in this case 'pyvcf' is crucial if you want the developer to find your question. I've edited your post to add this tag.

[inkprs]

Ok, any python solution?

[WouterDeCoster]

You could have a look at https://github.com/brentp/cyvcf2, which I prefer for vcf parsing. The variants have a .genotype attribute.