I am using the GATK and Mutect2 versions: gatk-package-18.104.22.168
I have for the same sample both short reads and long reads and I am looking for somatic mutations in my data.
I have read the post Variant calling with PacBio HiFi reads but I still have a problem with my run.
I did not combine the two sequencing samples and compared Mutect2 output runs on them.
Per sample, my pipeline (1) marks and removes duplicates using gatk MarkDuplicates with -REMOVE_DUPLICATES true. This steps removes about 15% of the reads from both samples. Then (2) I make a new index file for the "no duplicated reads bam" file. Last (3) I run Mutect2.
While for the short reads mapped with bwa I get about variants, for the hifi reads mapped with minimap2 I don't get any variants.
Could you please direct me to what I can do on the hifi minimap2 input differently?
Thank you so much,
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