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Indel shown in IGV not called by GATK 4.0

The code I used to produce g.vcf file is

gatk HaplotypeCaller -R /work7_P1/GATK_RegionCall/IRGSP-1.0/IRGSP-1.0_genome.fasta -I /work7_P1/GATK_RegionCall/Bam_SortIndex/CX227.bam -O /work7_P1/GATK_RegionCall/Variant_call/CX227.g.vcf -L chr01 -ERC GVCF --max-alternate-alleles 25

In the g.vcf file, site 4886943 is marked as reference allele

chr01   4886940 .       G       <NON_REF>       .       .       END=4886942     GT:DP:GQ:MIN_DP:PL      0/0:19:39:19:0,39,585
chr01   4886943 .       T       <NON_REF>       .       .       END=4886943     GT:DP:GQ:MIN_DP:PL      0/0:18:18:18:0,18,270
chr01   4886944 .       A       <NON_REF>       .       .       END=4886951     GT:DP:GQ:MIN_DP:PL      0/0:15:0:13:0,0,93
chr01   4886952 .       A       <NON_REF>       .       .       END=4886952     GT:DP:GQ:MIN_DP:PL      0/0:15:10:15:0,10,515

However, when I checked my bam file, I can see an 8bp deletion, which is correct(or which has the most reads supported)

Then I check my final vcf file and it is also marked as reference allele supported by 18 reads

chr01   4886943 .       TAGAGAGAGAG     TAG,TAGAGAGAGAGAGAGAG,TAGAGAG,TAGAG,TAGAGAGAGAGAGAG,T   279066.38       .       AC=963,65,1008,117,62,44;AF=0.167,0.011,0.175,0.020,0.011,7.644e-03;AN=5756;BaseQRankSum=-3.190e-01;DP=23753;ExcessHet=-0.0000;FS=8.590;InbreedingCoeff=0.8526;MQ=58.21;MQRankSum=0.00;QD=27.26;ReadPosRankSum=0.00;SOR=2.043   GT:AD:DP:GQ:PGT:PID:PL:PS       0/0:18,0,0,0,0,0,0:18:18:.:.:0,18,270,18,270,270,18,270,270,270,18,270,270,270,270,18,270,270,270,270,270,18,270,270,270,270,270,270

Why can't GATK recognize this kind of Indel or provide any evidence about the indel?

Answers

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