Question

Allele specific reads

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8.1 years ago

prasoon.agarwal ▴ 10

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 • 1.9k views

ADD COMMENT • link updated 8.1 years ago by GouthamAtla 12k • written 8.1 years ago by prasoon.agarwal ▴ 10

score 2 · Answer 1 · 2016-04-02

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8.1 years ago

GouthamAtla 12k

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

ADD COMMENT • link 8.1 years ago by GouthamAtla 12k

score 0 · Answer 2 · 2016-04-02

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8.1 years ago

Devon Ryan 104k

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.

ADD COMMENT • link 8.1 years ago by Devon Ryan 104k

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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.

ADD REPLY • link 8.1 years ago by prasoon.agarwal ▴ 10

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This previous question deals with phasing: What Are Phased And Unphased Genotypes?

ADD REPLY • link 8.1 years ago by Devon Ryan 104k