merging of multi samples tabix and bzipped vcf files into one vcf file using Perl program.

Question

[aarvaBioinfo]

HI, I want to merge multi sample individual files ( vcf1.vcf.gz, vcf2.vcf.gz.............vcf30.vcf.gz) which has is tabix index and compressed by bgzipp so Is here anyone know the Perl Program for this.

[cpad0112]

Is perl mandatory in merging VCF files? You can use bcftools to merge vcfs. You can also use picard's MergeVCFs or GATK combinevariants walker.

[finswimmer]

Here the link to the current version: http://www.htslib.org/doc/bcftools.html#concat

[aarvaBioinfo]

Thank you cpad0112 for valuable links :) actually I need to do this by using Perl

[cpad0112]

Then you can use perl API from VCFtools posted by JC below.

Answer 1

[JC]

You can use VCFtools https://vcftools.github.io/index.html, it also contains Perl modules

[aarvaBioinfo]

thank you JC for links.