HapCutToVcf

Overview

Group: VCF/BCF

Converts the output of HAPCUT (HapCut1/HapCut2) to a VCF.

The output of HAPCUT does not include all input variants, but simply those variants that are in phased blocks. This tool takes the original VCF and the output of HAPCUT, and produces a VCF containing both the variants that were phased and the variants that were not phased, such that all variants in the original file are in the output.

The original VCF provided to HAPCUT is assumed to contain a single sample, as HAPCUT only supports a single sample.

By default, all phased genotypes are annotated with the PS (phase set) FORMAT tag, which by convention is the position of the first variant in the phase set (see the VCF specification). Furthermore, this tool formats the alleles of a phased genotype using the | separator instead of the / separator, where the latter indicates the genotype is unphased. If the option to output phased variants in GATK’s ReadBackedPhasing format is used, then the first variant in a phase set will have / instead of | separating its alleles. Also, all phased variants will have PASS set in its FILTER column, while unphased variants will have NotPhased set in their FILTER column. Unlike GATK’s ReadBackedPhasing, homozygous variants will always be unphased.

More information about the purpose and operation of GATK’s Read-backed phasing, including its output format, can be found in the GATK Forum

Additional FORMAT fields for phased variants are provided corresponding to per-genotype information produced by HapCut1:

1. The RC tag gives the counts of calls supporting allele0 and allele1 respectively.
2. The LC tag gives the change in likelihood if this SNP is made homozygous or removed.
3. The MCL tag gives the maximum change in likelihood if this SNP is made homozygous or removed.
4. The RMEC tag gives the reduction in MEC score if we remove this variant altogether.

Additional FORMAT fields for phased variants are provided corresponding to per-genotype information produced by HapCut2:

1. The PR tag is 1 if HapCut2 pruned this variant, 0 otherwise.
2. The SE tag gives the confidence (log10) that there is not a switch error occurring immediately before the SNV (closer to zero means that a switch error is more likely).
3. The NE tag gives the confidence (log10) that the SNV is not a mismatch (single SNV) error (closer to zero means a mismatch is more likely).

HapCut2 should not be run with --call-homozygous as the genotypes may be different than the input and so is not currently supported.

For more information about HapCut1, see the source code or paper below. source code: https://github.com/vibansal/hapcut HapCut1 paper: An efficient and accurate algorithm for the haplotype assembly problem Bioinformatics. 2008 Aug 15;24(16):i153-9.

For more information about HapCut2, see the source code below.

Arguments

Name	Flag	Type	Description	Required?	Max # of Values	Default Value(s)
vcf	v	PathToVcf	The original VCF provided to HapCut1/HapCut2.	Required	1
input	i	FilePath	The file produced by HapCut1/HapCut2.	Required	1
output	o	PathToVcf	The output VCF with both phased and unphased variants.	Required	1
gatk-phasing-format	r	Boolean	Output phased variants in GATK’s ReadBackedPhasing format.	Optional	1	false
fix-ambiguous-reference-alleles		Boolean	Fix IUPAC codes in the original VCF to be VCF 4.3 spec-compliant (ex ‘R’ -> ‘A’). Does not support BCF inputs.	Optional	1	false