Question: merging of multi samples tabix and bzipped vcf files into one vcf file using Perl program.
1
gravatar for aarvaBioinfo
14 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 • 483 views
ADD COMMENTlink modified 14 months ago by JC8.2k • written 14 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 14 months ago • written 14 months ago by cpad011211k

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

ADD REPLYlink written 14 months ago by finswimmer12k

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

ADD REPLYlink written 13 months ago by aarvaBioinfo10

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

ADD REPLYlink written 13 months ago by cpad011211k
1
gravatar for JC
14 months ago by
JC8.2k
Mexico
JC8.2k wrote:

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

ADD COMMENTlink written 14 months ago by JC8.2k

thank you JC for links.

ADD REPLYlink written 13 months ago by aarvaBioinfo10
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