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Merging Vcf Chunks After Gatk Unifiedgenotyper?

What is the recommended way of merging the resulting vcf files when running GATK UnifiedGenotyper version 1.6 on chunks of, say, 10M?

I've got files like this:

chr10.0001.vcf
chr10.0002.vcf
chr10.0003.vcf
chr10.0004.vcf
chr10.0005.vcf
chr10.0006.vcf
chr10.0007.vcf
chr10.0008.vcf
chr10.0009.vcf
chr10.0010.vcf
chr10.0011.vcf
chr10.0012.vcf
chr10.0013.vcf
chr10.0014.vcf

where the first file is the first 10M, the second is the following 10M, etc. and I want to end up with a since chr10.vcf file that includes all the ones above.

Is just doing find -name "chr10.*" | sort | xargs cat on the files enough?

gatk vcf vcftools
• 4,661 views • link
updated by Jorge Amigo Jorge Amigo • written by 14134125465346445 14134125465346445

2 answers

use vcf-concat : http://vcftools.sourceforge.net/perl_module.html#vcf-concat

• 304 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

if you are working with GATK you may find the CombineVariants walker very useful. the first example mentioned in the documentation shows how you can merge any set of .vcf files by adding them through the --variant option:

java -Xmx2g -jar GenomeAnalysisTK.jar \
-R ref.fasta \
-T CombineVariants \
--variant input1.vcf \
--variant input2.vcf \
-o output.vcf \
-genotypeMergeOptions UNIQUIFY
• 166 views • link
written by Jorge Amigo Jorge Amigo

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