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Old 09-26-2016, 02:12 PM   #1
Jon17
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Location: Indiana

Join Date: Jun 2016
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Default Have variant call file, need to do snp counts (methylation counts)

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 Cís and Cís converted to Tís in capture target regions (this is sequence capture), both strands.

TOTAL_C_METHYLATED Total number of Cís in CpG context that were methylated

PCT_C_METHYLATED Percent of Cís 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 Cís methylated

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