mutect2 can not identify the indel that can be found in bam file

Question

[zhao03]

i used mutect2 calling a pair of sample of WES. i can see the indel in bam file ,but the result of mutect2 did not have it. form the bam of mutect2 result, i can see the total read of this indel is 282, the number read of DEL is 52, INS is 32.

the command is

nohup java -jar /home/D/ref/gatk/gatk-package-4.1.4.1-local.jar  Mutect2 \

-R /home/D/ref/hg19/ucsc.hg19.fasta \

-I /home/D/zjj/colon_wes/Nova501-H6K819125-20219002-T192V1Plus-AC-20200303cap98-20R03595.bam -normal Nova501-H6K819125-20219002-T192V1Plus-AC-20200303cap98-20R03595 \

-I /home/D/zjj/colon_wes/Nova501-H6K819125-20219002-T192V1Plus-AC-20200303cap67-20R03641.bam -tumor Nova501-H6K819125-20219002-T192V1Plus-AC-20200303cap67-20R03641 \

-L /home/D/zjj/colon_wes/T192V1_plus_loci.bed \

-O output.vcf \

-bamout 2_tumor_normal_m2.bam &

[ATpoint]

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