README.md

mendacity

simply-specified tests for inheritance models.

syntax

All tests are specified in YAML format.

Each test file specifies one pedigree and a number of tests for that pedigree.

Depths, GQ's, PL's, etc are not specified only the number of alternates:

genotype	n-alts	name
0/0	0	HOM-REF
0/.	0	HOM-REF
./0	0	HOM-REF
0/1	1	HET
./1	1	HET
1/.	1	HET
1/1	2	HOM-ALT
./.	-1	UNKNOWN

For decomposed alleles ./. can also be 0-alts.

A simple test for a trio of mom, dad, proband looks like:

  name: ar-test
  description: simple autosomal-recessive
  alts: [[1, 1, 2]] 
  modes: ["autosomal-recessive"]
  not-modes: ["autosomal-dominant"]

where:

• modes defines what inheritance modes this meets
• not-modes defines what inheritance modes this must not meet

For this trio, the yaml specifying the pedigree is:

pedigree:
- &dad
    id: Fred
    status: unaffected
    sex: male
- &mom
    id: Alice
    status: unaffected
    sex: female
-
    id: Bobby
    status: affected
    sex: female
    father: *dad
    mother: *mom

and the test-cases are:

cases:
-
  name: ar-test
  description: simple autosomal-recessive
  alts: [[1, 1, 2]]
  modes: ["autosomal-recessive"]
  not-modes: ["autosomal-dominant"]
-
  name: comp-het-example
  description: >
     requires 2 alts from different parents
     and alleles.                                                                                                                                                                      
  modes: ["compound-het"]
  alts: [[0, 1, 1], [1, 0, 1]]

constraints

• status ∈ unaffacted|affected|unknown|carrier
• sex ∈ male|female|unknown
• Modes ∈ autosomal-dominant|autosomal-recessive|compound-het|de-novo|x-linked-recessive|x-linked-dominant|x-linked-de-novo

VCF/PED

A VCF and PED pair can be created from a test-case yaml with:

python mendacity/tovcf.py tests/transmitted-dn.yaml

This will create transmitted-dn.vcf and transmitted-dn.ped