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GenotypeGVCFs wgs samples

I have about 130 wgs vcf files (created by GATK HaplotypeCaller). When I try to use GenotypeGVCFs, it goes out of memory. Can I split the sample vcf files by chromosome, call using GenotypeGVCFs, and then combine the chromowise results?

For example, can I do something like (for chr5, where ‘mysamplelist.list’ contains filepaths for sample vcf files):

java -Xmx32g -jar GenomeAnalysisTK.jar —L 5 -R myref.fa -T GenotypeGVCFs —variant mysamplelist.list -o out_chr5.vcf

and then combine the ‘out_chr{1..22}.vcf’ files using CombineGVCFs?

Or how else should I go about doing this?




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