Question: merging of multi samples tabix and bzipped vcf files into one vcf file using Perl program.
1
gravatar for aarvaBioinfo
8 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 • 271 views
ADD COMMENTlink modified 8 months ago by JC7.4k • written 8 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 8 months ago • written 8 months ago by cpad011211k

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

ADD REPLYlink written 8 months ago by finswimmer10k

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

ADD REPLYlink written 8 months ago by aarvaBioinfo10

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

ADD REPLYlink written 8 months ago by cpad011211k
1
gravatar for JC
8 months ago by
JC7.4k
Mexico
JC7.4k wrote:

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

ADD COMMENTlink written 8 months ago by JC7.4k

thank you JC for links.

ADD REPLYlink written 8 months ago by aarvaBioinfo10
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