Question: Calling allele-specific methylation from bisulfite sequencing reads
gravatar for Jautis
4.0 years ago by
United States
Jautis290 wrote:

I have mapped bisulfite sequencing reads (RRBS) and a vcf file of genetic variants (called from low coverage sequencing). Can anyone suggest a pipeline for calling allele-specific methylation?


ADD COMMENTlink modified 4.0 years ago by dariober11k • written 4.0 years ago by Jautis290
gravatar for dariober
4.0 years ago by
WCIP | Glasgow | UK
dariober11k wrote:

I don't know if such a tool or pipeline exists off-the-shelf. If not, I think some scripting is required, probably using python/pysam java/htsjdk or other API to process bam files.

Essentially for each read spanning a variant and spanning one or more cytosines on the reference sequence you record whether the cytosine(s) are methylated or not (i.e. they are C or they have been converted to T) and you record whether the variant is a reference or an alternative allele. You need to record also the position of the cytosine(s) in genomic coordinates. (This strategy is not difficult but it might be a bit tricky to get right.)

ADD COMMENTlink written 4.0 years ago by dariober11k
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