get variant chromosome, start, and end position from vcf

Question

[fastdavid91]

Hi all,

I am need to understand how to extract the chromosome, start position, and end position for each variant in a vcf file. I have the vcf, and bam files really I need the position of the variant.

I thought maybe vcf tools would help, but my results don't make sense. Any help would be greatly appreciated. Thanks very much.

Answer 1

[Pierre Lindenbaum]

bcftools query -f '%CHROM:%POS-%END\n' in.vcf

[tushardave26]

Do we have any pythonic way of getting start and end positions of a variant from VCF file?

[Pierre Lindenbaum]

https://pyvcf.readthedocs.io/en/latest/API.html#vcf-model-record

[tushardave26]

Thank you Pierre.