If you are seeing an error, please provide(REQUIRED) :
a) GATK version used: 220.127.116.11
b) Exact command used:
/gatk/gatk Mutect2 --java-options "-Xmx8g" -O $1 -R $2 -I $3 -tumor "$TUMOR" -I $4 -normal "$NORMAL" -L $5
c) Entire error log:
If not an error, choose a category for your question(REQUIRED):
c) Why do I see (......)?
I am seeing a long deletions variant being called between two sets of bam reads with REF,ALT depth of 140,2 respectively. However this is in a gap between two sets of reads where there is literally zero read support for the variant (see blue bar at top in image representing the deletion).
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