I am using GATK to do SNPs calling from 140 RNAseq data. After variant calling of each sample with HaplotypeCaller, I get 140 g.vcf.gz files. Before perform the final joint genotyping through GenotypeGVCFs, I need to combine these 140 g.vcf.gz files into one. Beforehand, I prepare a gvcf file list with
ls hard_filtered/*_filtered.vcf.gz > gvcfs.list
And the command used for combining are:
gatk CombineGVCFs -R genome.fa --variant gvcfs.list -O cohort.vcf.gz
After running a very long time (~8 hours), the job finished (telling from top command), and the log file didn't show any error. However, I didn't see any output file. Is there anything I can do to fix this?
Thanks a lot.