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.
•
written
by
fastdavid91 •
bcftools query -f '%CHROM:%POS-%END\n' in.vcf
Do we have any pythonic way of getting start and end positions of a variant from VCF file?
Thank you Pierre.
Log in to answer this question.
