How to keep MAPQ on multiple mapping reads
We are using Gatk 4.1.4.1 to call somatic variant in the only tumor mode in hg38.
We performed sequencing through an amplicon-based targeted gene panel.
We are not able to call variants validated by other panels/pipelines in the whole gene U2AF1 (chr21:43,094,647-43,094,686) because reads have all MAPQ = 0 probably due to multi-mapping.
In hg38, U2AF1 has an exact copy called U2AF1L5 (chr21:6,484,623-6,499,248).
We tried to disable read quality filters such as --disable-tool-default-read-filters true, but mutect2 did not analyze reads with MAPQ=0.
Maybe we can act to Bwa-Mem so:
It is possible to keep MAPQ on multiple mapping reads? How do we act in the processing-for-variant-discovery-gatk4.wdl to change bwa-mem parameters?
or
It is possible to use bwa-mem only in some regions (from an interval list file) to reduce multi-mapping probability? Or it is possible to exclude some regions from alignment acting in the wdl file?
Thanks for the help.
Mat
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Hi MatZ,
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