Checkphase

Provided a reference and a query VCF/BCF file, Checkphase compares common biallelic variants from both files and gives a summary on switch errors (useful for haplotype phasing) and genotype errors (useful for genotype imputation). The tool uses Htslib to load the VCFs and to identify common sites.

Note: The reference and the query files must contain exactly the same samples.

Note: A different phase in both input files at a heterozygous site is only considered as a switch error if the phase at the previous common heterozygous site was equal. Otherwise, the path simply continues and the difference is therefore not another switch error. Futhermore, a phase difference at the first heterozygous position is considered as a switch in the maternal and paternal path (mat/pat switch) and not as a switch error.

The --stat switch continuously writes the progress in a file with the provided filename.

The --dump switch dumps for each sample the phase error positions to stderr.

Example output

Comparing two phasing outputs:

$ checkphase ref.vcf.gz query.vcf.gz

Input files:
  Reference: ref.vcf.gz
  Query:     query.vcf.gz
  Reference variants (from index): Mref = 8799
  Reference samples:               Nref = 500
  Query variants (from index):   Mquery = 8799
  Query samples:                 Nquery = 500

Passed samples check.
Checking common variants for phase and genotype errors... done.

Summary:

  Haploid ref samples:      0
  Haploid query samples:    0

  Reference variants:       8799
  Query variants:           8799
  Common variants:          8799
  Checked variants:         8799

  Excluded commons:         0
    Not biallelic in ref:   0
    Not biallelic in query: 0
    Alleles do not match:   0

  Ref/Alt swaps:            0
  Strand flips:             0
  Ref/Alt + Strand flip:    0

  Missing or unphased sites:
    Total missing in ref:        0
    Total missing in query:      0
    Total unphased het in ref:   0
    Total unphased het in query: 0

  Genotype errors (hard):
    Total genotype errors:     0
    Minimum genotype errors:   0
    Maximum genotype errors:   0
    Average gt err per sample: 0
    Minimum gt error rate:     0
    Maximum gt error rate:     0
    Average gt error rate:     0
    Standard GER deviation:    0
    GER variance:              0

  Switch errors:
    Total switch errors:       27855
    Minimum switch errors:     4
    Maximum switch errors:     379
    Average sw err per sample: 56
    Minimum sw error rate:     0.000454597
    Maximum sw error rate:     0.0430731
    Average sw error rate:     0.0063314
    Standard SER deviation:    0.00318695
    SER variance:              0.000220513
    Switch error free targets: 0
    Mat/Pat switches:          251

Summarize information

The bash script checkphase_extract can be used to generate a CSV file from several outputs of Checkphase, e.g. from several chromosome files.

In addition, the bash script checkphase_summary summarizes the outputs of several Checkphase runs.

Both scripts use AWK in the background.