I try to use gatk haplotypecallerspark. I have gatk 18.104.22.168. My data are human WGS (40X). Each bam is arround 100 Go. I try this command, but it stops less than 2 minutes after begining (i don't see what is the error in the log file, or at least i didn't understand) :
gatk --java-options "-Xmx40G" HaplotypeCallerSpark \ -R /Path/ref.fa \ -I /path/input.bam \ -O /path/output.g.vcf \ -ERC GVCF \ --tmp-dir /path/tmp \ -- \ --spark-master local
Someone have an idea of how i can use haplotypecaller? If i use the non spark haplotypecaller it will be very long? I have 74 WGS.
If you want to see the log file it's here
Thank's in advance,