Dear Sir/Madam,
I'm running the combineGVCFs in order to create batches of 100 GVCFs. The job is running perfectly, reading first of all the 100 files with the proper name, but once is the combined gVCF is generated the name of the 100 individuals is changed. Do someone knows what is going on? I saw that for each of my file a number (Variant1, Variant2.... Variant100) is assigned. That's the order that I can find it in the combined gVCF?
The command that I'm using is the following:
java -Xmx24G -jar /opt/GATK-3.5/GenomeAnalysisTK.jar -T CombineGVCFs -R ucsc.hg19.fasta --dbsnp dbsnp_137.hg19.vcf -V batch1 -o batch1_calling.g.vcf
Thank you in advance for your help.
Best wishes,
Jordi