Phased data

Phased data

genmod can handle phased vcf files. This information is used when checking the compound heterozygous inheritance pattern. If two variants are on the same phase they will not follow the pattern since they will only affect one of the transcripts.

If a variant is phased it is denoted in the genotype call with a pipe instead of a backslash.

• Unphased call: '0/1'
• Phased call: '0|1'
• A collection of censequtive phased variants makes a haploblock.
• The haploblocks are broken when a unphased call is seen.