Prepare genofile

The first required input for RABBIT is a genofile, which must be a vcf file with extension ".vcf" or ".vcf.gz". The version of vcf file format must be v4.1 or above.

Include genetic map

A vcf file contains the physical map in the first three columns: #CHROM, POS, ID. We can provide the genetic map by adding keywords LINKAGEGROUP and POSCM in the INFO column, assuming the linkage group is #CHROM.

#fileformat=VCFv4.3
#INFO=<ID=LINKAGEGROUP,Number=1,Type=String,Description="Linkage group in genetic map">
#INFO=<ID=POSCM,Number=1,Type=Float,Description="Genetic marker position in centiMorgan">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO    FORMAT	P1	P2 Offspring1
chr1	34522	snp1	N	.	.	.	LINKAGEGROUP=LG1;POSCM=0.0   GT  0/0 1/1 ./1
chr1	54347	snp2	N	.	.	.	LINKAGEGROUP=LG1;POSCM=1.3   GT  1/1 0/0 0/1
chr1	66710	snp3	N	.	.	.	LINKAGEGROUP=LG1;POSCM=1.5   GT  0/0 ./. 0/0

See MagicMap.magicmap for constructing the genetic map. See MagicBase.resetmap for resetting the markermap for a vcf file.

Inferred error rates

Marker specific error rates can be inferred during genotype imputation. These estimates are saved in the INFO column using additional keywords. Denote by sequence allelic balance the expected ratio of number of reads for the reference allele to the number of reads for the alternative allele. We only consider heterozygous allelic balance, which is 1/2 if there is no allelic balance bias. For example, the INFO for snp2 could be "LINKAGEGROUP=LG1;POSCM=1.3;FOUNDERERROR=0.005;OFFSPRINGERROR=0.012;SEQERROR=0.0008;ALLELEBALANCEMEAN=0.48;ALLELEBALANCEDISPERSE=0.1;ALLELEDROPOUT=0.0".

  • FOUNDERERROR: allelic error rate in founders.
  • OFFSPRINGERROR: allelic error rate in offspring.
  • SEQERROR: sequence based error rate.
  • ALLELEBALANCEMEAN: mean sequence allelic balance among offspring at a marker.
  • ALLELEBALANCEDISPERSE: overdispersion for the distribution of sequence allelic balance among offspring.
  • ALLELEDROPOUT: 0- and 1-inflation for the distribution of sequence allelic balance among offspring.

These keywords are also explained in the beginning comment lines of the vcf file.