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Allele specific reads

I have SNVs from the patients. And I also have the ATAC-seq data from the same patient. Now I am looking for extracting allele specific reads using the SNV positions. I was wondering if there is any tool available for this purpose. Can we do this using samtools? Any suggestions will be highly appreciated?

snv allele specific reads atac-seq
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updated by GouthamAtla GouthamAtla • written by prasoon.agarwal • prasoon.agarwal

2 answers

You could also use ASEReadCounter of GATK in addition to the tools mentioned by Devon.

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written by GouthamAtla GouthamAtla

Any of the normal allele-specific tools (e.g., lapels and then suspenders) should work. Not that you'll need to randomly assign each heterozygous allele to one genome. The results will likely be better if you try to phase the variants first.

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written by Devon Ryan Devon Ryan

Thanks for your suggestions. Actually I am very new to this field. What do you mean by phasing the variants. I have already masked the genome using the locations of the variants.

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written by prasoon.agarwal • prasoon.agarwal

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