I am using GATK4 version 184.108.40.206
I searched the forum and did not find a similar question. I apologize if this is already answered.
I have a ref genome and 43 low coverage genomes with 23 chromosomes. Do I need to run Haplotypecaller for each chromosome and create 23 separate GenomicDGImport databses? I cannot seem to see a way to generate a single database that includes all chromosomes.
I have written a shell script to run this, the GATK4 commands are as follows:
HaplotypeCaller="gatk --java-options "-Xmx200g" HaplotypeCaller \
-R $Ref \
-I $f \
-L $chrom \
--genotyping-mode DISCOVERY \
--emit-ref-confidence GVCF \
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