Question: Spliting a VCF for some genotypes
0
gravatar for umermehar10
10 weeks ago by
umermehar1010
umermehar1010 wrote:

Dear All I have a VCF file of 250 genotypes developed using HaplotypeCaller at GATK tools. now I want to split a set of 200 individuals as new vcf file. Is is possible using GALAXY. Kindly help me in this regard by suggesting a workable solution if possible in galaxy.

vcf galaxy • 112 views
ADD COMMENTlink modified 10 weeks ago • written 10 weeks ago by umermehar1010
1
gravatar for umermehar10
10 weeks ago by
umermehar1010
umermehar1010 wrote:

Thank You very much GUY Reeves for this valuable suggestion.

ADD COMMENTlink written 10 weeks ago by umermehar1010
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gravatar for Guy Reeves
10 weeks ago by
Guy Reeves1.0k
Germany
Guy Reeves1.0k wrote:

Hi This tool should do it 'VCFselectsamples: Select samples from a VCF dataset'. there are others. It may help when looking for tools to be aware of VCF terminology specifically that individuals = samples. 'genotypes' could mean a few different things,

Personally I use this galaxy tool 'Select Variants from VCF files' but this is not available on Usegalaxy.org (it is part of GATK package but it is a stand alone tool). Cheers

guy

ADD COMMENTlink modified 10 weeks ago • written 10 weeks ago by Guy Reeves1.0k
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