Question: merging of multi samples tabix and bzipped vcf files into one vcf file using Perl program.
1
gravatar for aarvaBioinfo
23 months ago by
aarvaBioinfo10
aarvaBioinfo10 wrote:

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.

vcf perl • 791 views
ADD COMMENTlink modified 23 months ago by JC10k • written 23 months ago by aarvaBioinfo10
1

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.

ADD REPLYlink modified 23 months ago • written 23 months ago by cpad011213k

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

ADD REPLYlink written 23 months ago by finswimmer13k

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

ADD REPLYlink written 23 months ago by aarvaBioinfo10

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

ADD REPLYlink written 23 months ago by cpad011213k
1
gravatar for JC
23 months ago by
JC10k
Mexico
JC10k wrote:

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

ADD COMMENTlink written 23 months ago by JC10k

thank you JC for links.

ADD REPLYlink written 23 months ago by aarvaBioinfo10
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