Jan 13 2020

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The reference and target VCF files are each required to have data for at least 20 individuals so that the statistical tests performed by the conform-gt program give reasonable results.

The conform-gt program will:

  1. Find corresponding VCF records in the target and reference files.
  2. Exclude target VCF records which cannot be matched to any reference VCF record.
  3. Exclude target VCF records whose chromosome strand cannot be determined. The conform-gt program makes use of allele frequency and inter-marker correlation to determine chromosome strand in ambiguous cases.
  4. Adjust target VCF records so that chromosome strand and allele order match the VCF reference file.

VCF records are permitted to have multiple non-reference alleles.

Running conform-gt

To use conform-gt, enter the following command at the command line prompt:

java -jar conform-gt.jar arguments

where arguments is a space-separated list of parameters, each expressed as parameter=value.

Required Parameters

Optional Parameters

The conform-gt program first finds pairs of VCF records (one record each from the reference and target data) that correspond to the same variant. The match command line argument determines whether VCF records are matched using the ID field or the POS field. Two matched VCF records have an identical identifier (if match=ID ) or an identical POS field (if match=POS ). In either case, two records are matched only if the alleles in the target VCF record or in the strand-flipped target VCF record are a subset of the alleles in the reference record.

Once a target record is matched to the reference record, three sources of information are used to determine whether the chromosome strand in a reference and a target VCF record are identical or opposite: alleles, REF allele frequency, and inter-marker correlation of REF allele dosage.

If strict=true the orientation of the chromosome strand in a reference and a target VCF record (identical or opposite) is determined only if a) allele frequency or inter-marker allele correlation provide strong support for a particular orientation (identical or opposite), and b) the evidence from each source of information (allele labels, frequency, and correlation) is consistent.

Output files

Two output files are produced:

  • a VCF file (.vcf.gz) containing modified target VCF records that are matched to the reference VCF file.
  • a log file (.log) containing one header line and one line for each record in the input VCF file.

Each line of the output log file has 10 tab-delimited fields.

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