Have variant call file, need to do snp counts (methylation counts)

Question

[Jon17]

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

[WouterDeCoster]

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.

[Jon17]

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