Appending multiple vcf

If you have multiple vcf files split by chromosome from the same samples, this is the case when performing joint variant calls of multiple samples in GATK. At the end of the day, if you want to have a single vcf file from this project, CatVariants tool (a command line tool in GATK) is pretty fast. Although I think this might be just the case of simple cat of multiple files except the vcf header, this tools still come in handy especially when you already have GATK installed.

java -cp GenomeAnalysisTK.jar \
-R hg19.fa \
-V chrM.normal.vcf.gz \
-V chr1.normal.vcf.gz \
-V chr2.normal.vcf.gz \
-V chr3.normal.vcf.gz \
-V chr4.normal.vcf.gz \
-V chr5.normal.vcf.gz \
-V chr6.normal.vcf.gz \
-V chr7.normal.vcf.gz \
-V chr8.normal.vcf.gz \
-V chr9.normal.vcf.gz \
-V chr10.normal.vcf.gz \
-V chr11.normal.vcf.gz \
-V chr12.normal.vcf.gz \
-V chr13.normal.vcf.gz \
-V chr14.normal.vcf.gz \
-V chr15.normal.vcf.gz \
-V chr16.normal.vcf.gz \
-V chr17.normal.vcf.gz \
-V chr18.normal.vcf.gz \
-V chr19.normal.vcf.gz \
-V chr20.normal.vcf.gz \
-V chr21.normal.vcf.gz \
-V chr22.normal.vcf.gz \
-V chrX.normal.vcf.gz \
-V chrY.normal.vcf.gz \
-out normal.vcf.gz \

Check out the catVariant tools page for more detail:


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