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Insertion Homozygous but heterozygous in BAM files
I have some troubles with insertion variation. In my VCF file it is flagged as homozygous (1/1) but on my BAM file it appears heterozygous.
I generated BAM output file from HaplotypeCaller but it is the same thing.
I join the IGV snapshot. The top track is bam before HC et the bottom track is bam after HC.
Why if the depth is 34 and the insertion is counted 23 this variant is homozygous ?
For information I use GATK 3.5 and follow the guidelines.
The line in the VCF :
17 8245561 rs145968386 T TTTTA 1098.73 . AC=2;AF=1.00;AN=2;DB;DP=34;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.95;MQ0=0;QD=28.15;SOR=1.708 GT:AD:DP:GQ:PL 1/1:0,23:23:78:1136,78,0
Thank you !