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missing mutation in TP53

BogdanBogdan Palo Alto, CAMember ✭✭

Dear all,

we have been doing a WES analysis, and we have used MUTECT2 to call the mutations in a situation where we had :
1) -- a tumor sample
3) - unpaired 3 germline samples (that 've pooled together)

although we identify many cancer mutations by using this strategy, and exclude some germline variants, MUTECT2 apparently misses a mutation in TP53 (here attached an image in IGV). The MUTECT2 calling procedure is shown below.

If I may ask please, and if you could please advise, are there any changes I shall make in order to capture the mutation ?

$GATK \
-T MuTect2 \
-R $REFERENCE \
-L $CHR \
--cosmic $COSMIC76 \
--dbsnp $DBSNP138 \
-I:normal $NORMAL_MD_GATK \
-I:tumor $TUMOR_MD_GATK \
-o "vcf.${TUMOR_MD_GATK%.bam}intervals${CHR}vs${NORMAL_MD_GATK%.bam}.analysis-MUTECT2.vcf" \
--disable_auto_index_creation_and_locking_when_reading_rods

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