Hi all,
we use samtools for variant calling and the results always looked
good.
Now, we noticed that samtools 1.1 misses a pretty clear indel in one of
our samples.
It is a 6-base deletion combined with a 7-base insertion, which in sum
leads to a frameshift.
The 151pb paired-end reads were produced on an Illumina MiSeq. Haloplex
enrichment was used for the library preparation (amplicon-based).
The BAM file and Makefile with the commands and parameters can be
downloaded here:
https://docs.google.com/uc?export=download&id=0B-iHdfk93LueVGQ2bTVUMTJSZVE
Other callers, like FreeBayes and GATK HC can call the variant.
Is this a bug in samtools? Or do we need to set special parameters to
call this variant?
Thanks,
Marc
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