I have question regarding calling of SNPs at the end of read.
We do amplicon sequencing. We are normally using combination of HaplotypeCaller and UnifiedGenotyper but we would like to use only the latest HaplotypeCaller. We have problem calling SNPs at the end of the read (as you can see at figure below). I tried "recover-all-dangling-branches" option but it did not help (tried also with gatk3 and gatk4 haplotypecaller). UnifiedGenotyper has no problem to call this SNP. This SNP is covered only by one read (but well covered). Any suggestions please?
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