Do we have Alt Aware peak calling tools also?
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4.4 years ago

Hi! I am relatively new to ChipSeq data analysis. Having worked in WGS data analysis, I am aware that it's wise to call Variants in alt aware manner, I am however unsure if same applies in PeakCalling or not (I also searched about alt aware peak calling but didn't get any result). I know from this article that Alternative loci are not meant to represent all variation within a population, but rather provide an immediate solution for adding sequences missing from the chromosome assembly. Keeping this information in mind, aligning reads in an alt unaware manner and then calling peaks might be misleading, I presume.

I learned bwa is the only tools currently that does read alignment in alt aware manner. I wish to know if there are more. Also, will alignment in alt aware manner hold relevance in Histone ChipSeq data analysis or not.

All kinds of inputs are welcomed.

ChIP-Seq alignment genome • 1.1k views
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I believe that several mappers are both alt and variant aware. HISAT is one. BWA can be run as alt aware. Certainly there are probably advantages in using these to map your ChIP-seq reads, athough how much difference it will make I have no idea. Might make a nice little benchmarking project.

I know of no peak-calling that is alt aware, but I'm happy to be corrected.

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And after peak-calling, you will want to annotate. That might be even more challenging than peak calling.

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Thanks. If I find something interesting, I will share it in this thread.

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it's wise to call Variants in alt aware manner

Most variant callers are still not alt-aware. GRCh38/hg38 was released more than 5 years ago and that was supposed to open the gates to all the alt-aware methods.

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