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Mutect2 indel alignment issues

Hi,

I have recently began testing Mutect2 for the analysis of single tumour samples. Most of the tools seem to work as expected however I have an issue with a particular indel. It is a 16 bp indel (16bp del with 1bp insertion) that the software is recognising as 2 indels of 7bp and 8bp separated by a single bp (screenshot attached).

I have read the documentation and the only parameter I can identify that might have any impact is `--max-mnp-distance' and I have set this to 0, 3 or 5 in testing but it has had no effect on the alignment or variant calling.

Are there any parameters or post-analysis steps I can apply to correct this?

Thanks,
Cathal

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Answers

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @cathalobrien

    Adjusting`--max-mnp-distance' will not help in this case. This has to do with Smith-Waterman alignment parameters that are hardcoded into GATK. It is an effect of the underlying alignment algorithm and not the tool parameters it self. Based on the penalty scores SW algorithm chooses this alignment.

  • cathalobriencathalobrien irelandMember

    Thanks @bhanuGandham

    I assume there is no way to modify the Smith-Waterman gap alignment parameters?

    Would you be aware of any tools that can be applied post Mutect2 to combine mutations/alignments into a single variant?

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    I assume there is no way to modify the Smith-Waterman gap alignment parameters?

    No there isn't it is hardcoded into GATK

    Would you be aware of any tools that can be applied post Mutect2 to combine mutations/alignments into a single variant?

    Not that I am aware of.

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