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2.9 years ago
Hyeong Seok
•
0
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