Hi I am new to bioinformatics.

Now I am on WES for PDAC patients.

During the process of GATK mutect2, I checked my vcf output file (unfiltered) and found that it has data on only chr 1.

But when I am doing the sequencing, all chromosomes are on the process.

Do you have any idea about this?

I use this command

gatk Mutect2 --native-pair-hmm-threads 12 -R (Reference.fasta) -I (*.removed.sorted.bam) --max-mnp-distance 0 -O (*.vcf.gz)

Thank you