ref: Solar User's Guide
Input Files
The following files are required:
- pedigree file
- marker file
- phenotype file
- map file
- freq file (optional, if not given, frequencies are estimated)
Except for the map and frequency file, comma-separated values (CSV) format is
used and the first row should contain variable names.
Pedigree File
- Required fields: id, fa, mo, sex.
- Optional fields: famid, mztwin, hhid.
- The ordering and the names of the fields are significant.
- Sex is coded 1/2 or M/F. Other values (e.g., missing) are not allowed.
- 0 is allowed for missing parent ID.
famid is required if there are duplicated ids.
Marker File
- Require field: id
- Optional field: famid
- Markers: M1, M2, ...
- Marker alleles are coded as: 123/456.
- Blank or 0/0 or -/- are treated as missing.
Phenotype File
- Require field: id
- Optional field: famid
- Traits and covariates: T1, T2, ...
- Blank field indicates missing data.
Map File
- The map file is spaced delimited.
- First line: chromosom_number map_type
- Other lines: marker_name marker_location_in_cM
- Map type can be 'Haldane' or "Kosambi' (the latter is the default).
- Each map file can only be used for markers on a single chromosome.
Freq File
- The freq file is spaced delimited.
- All lines: marker_name all_1_name freq all_2_name freq ...
- Allele frequencies must sum to 1.
Analysis
Load in Files
load pedigree solar.ped
load phenotype solar.phn
load markers solar.mrk
load map solar.map
load freq solar.frq
Multipoint IBD Calculation Using Merlin
mibd prep merlin
- Run merlin using the command in
mlmibd.cmd (created in current directory).
It might be advisable to run merlin in another directory (and the IBD file
can be reused).
sh mlmibd.cmd
- Import the IBD probabilities into Solar. 1 is the chromosome number.
mibddir .
mibd import merlin 1
Multipoint scan
model new
trait T1 T2
polygenic