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BD2KGenomics / brca-pipeline

This repo is deprecated! Please use https://github.com/BD2KGenomics/brca-exchange
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Remap UMD to hg19 and collapse samples for a variant into single vcf rows #23

Closed MollyZhang closed 9 years ago

maximilianh commented 9 years ago

I've added a script vcfMerge to the repo that does this. Note that my google reflexes are bad, there are already scripts out there that do almost the same thing, see https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_variantutils_CombineVariants.php

http://vcftools.sourceforge.net/htslib.html#merge http://vcftools.sourceforge.net/perl_module.html#vcf-merge

melissacline commented 9 years ago

That's great - Jing will be really happy to hear this!

On Thu, May 21, 2015 at 6:00 AM, Maximilian Haeussler < notifications@github.com> wrote:

I've added a script vcfMerge to the repo that does this. Note that my google reflexes are bad, there are already scripts out there that do almost the same thing, see

https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_variantutils_CombineVariants.php

http://vcftools.sourceforge.net/htslib.html#merge http://vcftools.sourceforge.net/perl_module.html#vcf-merge

— Reply to this email directly or view it on GitHub https://github.com/BD2KGenomics/brca/issues/23#issuecomment-104265801.