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
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