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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?