I was under the impression that the GATK IndelRealigner was supposed to left-align indels. I know that GATK has LeftAlignIndels and LeftAlignVariants, but those both output vcf files, and I would like an adjusted left-aligned bam file.
Attached is an example where two different deletion calls should clearly be collapsed into just one deletion. This alignment is after running GATK IndelRealigner.
Are there any other tools that can left-align indels in a bam file?
Attached is an example where two different deletion calls should clearly be collapsed into just one deletion. This alignment is after running GATK IndelRealigner.
Are there any other tools that can left-align indels in a bam file?
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