JiscaH / sequoia_notR

This Fortran program is the stand alone equivalent to the R package 'sequoia', and performs pedigree reconstruction from SNP data

General

This Fortran program is equivalent to the R package, except that the input & output does not go via R but via text files and command-line arguments. Very large datasets can be incredibly slow or even impossible to load into R; this non-R version works for up to 50K - 100K genotyped individuals.

Compilation

A Fortran compiler is needed, such as e.g. gfortran. In Windows you also need a linux emulator, e.g. cygwin (although other approaches may be possible).

gfortran -O3 Sequoia_SA.f90 -o sequoia

(NOTE: previous versions relied on -std=95 -fall-intrinsics, these flags are no longer necessary and will in fact cause compilation to fail)

File formats

Template files can be generated using the R package sequoia:

library(sequoia)
data(SimGeno_example, LH_HSg5)
SeqOUT <- sequoia(SimGeno_example, LH_HSg5, Err = 0.005, Module = "pre")
writeSeq(SeqList = SeqOUT, GenoM = SimGeno_example, 
         folder = "SequoiaFileTemplates")

Genotype data can be formatted from standard PLINK format as follows:

plink --bfile FileNameIN --recode A --out FileNameOUT
mv FileNameOUT.raw tmp.raw
cat tmp.raw | tr -s ' ' | cut -d ' ' -f2,7- > FileNameOUT.raw
sed -i '1d' FileNameOUT.raw 
sed -i 's/NA/-9/g' FileNameOUT.raw
rm tmp.raw

which

• recodes to 1 column per SNP, coded as 0/1/2 copies of minor allele, missing = NA
• drops columns 2--6 (family ID, sex, phenotype, etc)
• drops header row
• replaces missing value code NA by -9

Running

Parameter values are stored in SequoiaSpecs.txt. Many of these can be overruled on the command line, as described in the PDF manual.

./sequoia --geno geno.txt --par --ped --verbose

All command line options are shown with

./sequoia --help

Version

Its version will typically be functionally identical to the latest R package beta version. To obtain an older version, please send an email.