Frequently Asked Questions in GIGI
1.How do I choose framework markers?
Because the framework markers are assumed to be sparse, we want to
choose framework markers that are informative about which
chromosomes are being transmitted at the framework loci. First,
framework markers typed on a large number of subjects tend to be
most informative. Second, framework markers that are multi-allelic
tend to be more informative than di-allelic markers if they are
available. Third, if framework markers are SNPs, markers with high
minor allele frequencies in the sample tend to be more informative.
Fourth, framework markers should be moderately but not too dense
(eg. not denser than 1 marker per 0.3 cM because of concern about
MCMC mixing and violation of the assumption of Linkage Equilibrium)
If the framework markers are multiallelic, this spacing should be
greater, e.g., not denser than 1 marker per 2 cM for good MCMC
2.What do I have to be careful about the genetic map that I am
The map positions are in map distances based on the Haldane map
function, instead of Kosambi map function or sequence positions. If
this map is based on the Kosambi map function, the user will need to
convert the map positions to Haldane map function using an
appropriate conversion method. Also, since recombination fractions
are relative to each other, we strongly encourage the user to
generate both the framework map positions and the dense marker
positions at the same time.
3.Can GIGI process multiple pedigrees?
No. In version 1.01, GIGI can only process 1 pedigree at a time. For
this reason, gl_auto should also be run individually for each pedigree.
4.Can I use GIGI to impute genotypes on unrelated
5.What should I know when I use GIGI to impute genotypes on
Since there is no way to infer recombination on trios using unphased
genotypes, gl_auto produces an empty inheritance vectors file. From
the pedigree-meiosis file, GIGI recognizes that this inheritance
vectors file is empty but will proceed to impute genotypes. For
trios, imputing genotypes using GIGI is equivalent to imputing
genotypes conditional on the pedigree structure and minor allele
Information about linkage-disequilibrium is potentially useful for
genotype imputation on trios. Since the current version of GIGI does
not leverage information from linkage-disequilibrium, you may want
to use existing linkage-disequilibrium-based software that supports
imputation on trios (e.g. BEAGLE).