Link Search Menu Expand Document

Extract Methylation and Mutation Information

Make BED files

After generating the VCF file with both genetic and methylation information, beta values and coverage can be extracted to study the methylation levels at any sequenced CpGs. The following shows how to extract this information from the VCF file:

$ biscuit vcf2bed -t cg my_pileup.vcf.gz > my_pileup.bed

The -t flag can be used to retrieve mutation and other information, including

  • snp for SNP information
  • c for all cytosines
  • hcg for HCG (from NOMe-seq)
  • gch for GCH (from NOMe-seq)

Information about the sequence context for each row can be included by adding the -e flag to the command, while filtering out low coverage rows can be done using the -k flag.

For more help on available flags, run biscuit vcf2bed in the terminal or visit the vcf2bed help page.

Merge Neighboring C and G in CpG Context

At times, it might be desired that the methylation status be merged across the C and G in a CpG dinucleotide context. BISCUIT provides an easy-to-use subcommand, mergecg, to do this:

$ biscuit mergecg /path/to/my_reference.fa my_pileup.bed

For more help on available flags, run biscuit mergecg in the terminal or visit the mergecg help page.