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a chemotherapy site not appear in vcf and bam-out bam but apper in sorted.dedup.bam?

thanks a lot. I have a important question want to confirm with you.
a very important chemotherapy site not appear in vcf and bam-out bam but apper in sorted.dedup.bam as the figure shows.

the gayk.bam is the the argument --bam-out in haplotcaller, and the sorted.dedup is the bam in the forward steps that you kown as usual.

you can see here are 532 reads here, 228 reads support indel , 17 support del in the orted.dedup.bam.

I kown the --bam-out bam is a reassemble bam and stores the reliable variant gatk model trusts from the statistic.

you can see the region is a poly region, many TA, is this also a bad impact for the gatk model to make decision.

thanks a lot, I want to know how should I give out that site, because 6TA/7TA, 7TA/7TA, 6TA/6TA stands for different chemotherapy toxicity.

which genotype should I give of 6TA/7TA, 7TA/7TA, 6TA/6TA

thanks a lot

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