Question: Have variant call file, need to do snp counts (methylation counts)
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gravatar for Jon17
2.5 years ago by
Jon1710
Jon1710 wrote:

I'm using BisSNP to produce vcf files. Anyone know of a good way to calculate the following metrics? Any good tools to parse the VCF files?

TOTAL_C_IN_CpG_CONTEXT Total number of C’s and C’s converted to T’s in capture target regions (this is sequence capture), both strands.

TOTAL_C_METHYLATED Total number of C’s in CpG context that were methylated

PCT_C_METHYLATED Percent of C’s in CpG context that were methylated

TOTAL_C_POS_METHYLATED Total number of C positions in capture region (this is sequence capture), that had one or more C’s methylated

PCT_C_POS_METHYLATED Percent of C positions in capture region (this is sequence capture), that had one or more C’s methylated

bisulfite-seq methyl-seq • 803 views
ADD COMMENTlink modified 2.4 years ago by Biostar ♦♦ 20 • written 2.5 years ago by Jon1710

Hello jonathan.nowacki!

It appears that your post has been cross-posted to another site: http://seqanswers.com/forums/showthread.php?p=199295

This is typically not recommended as it runs the risk of annoying people in both communities.

ADD REPLYlink written 2.5 years ago by WouterDeCoster37k

Alright I'll stop doing that. Thanks for the heads up.

ADD REPLYlink written 2.5 years ago by Jon1710
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