We are using Gatk 220.127.116.11 to call somatic variant in the only tumor mode in hg38. We performed sequencing through an amplicon-based targeted gene panel.
Due to the presence of another copy of a gene in the reference genome hg38, we masked that region starting from .fasta supplied in the cloud bucket.
Then we create the index with
bwa index -a *.fasta
Unfortunately, the command did not create the .alt file. As a consequence, Mutect2 did not call variants in HRAS gene because the reads map also in an alternative locus and MAPQ became 0 due to multi-mapping.
How do we can create .alt file of a masked genome?
Thanks for the help
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