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PARAMFILE.txt
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PARAMFILE.txt
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## This is a parameter file for Zanardi program. Follow the specifics below.
## Please specify the variables required
## Only what comes after the "=" is retained, so include as many comments as you like.
## NOTES: ALL lines beginning with "#" will be skipped!
## DO NOT delete or modify ANY variable name (not even if you're not using the pgm!)
##
######
## History:
## Coded originally: Gabriele Marras & Ezequiel L. Nicolazzi (2015)
######
### ----------------------
### --- SOFTWARE PATHS ---
### ----------------------
### --- *ABSOLUTE* path to the required software for all the analyses within Zanardi
### --- If you don't have a required program installed please see README ( --download option)
PGM_PLINK=
PGM_FCGENE=
PGM_BEAGLE3=
PGM_BEAGLE4=
PGM_ADMIXTURE=
PGM_FIMPUTE=
### ---------------------------------------
### --- GENOTYPE & PEDIGREE INPUT FILES ---
### ---------------------------------------
### --- *ABSOLUTE* path preferred
SPECIES= COW
INPUT_PED= Example_data/example_PLINK_snp2000.ped,Example_data/example_PLINK_snp4000.ped
INPUT_MAP= Example_data/example_PLINK_snp2000.map,Example_data/example_PLINK_snp4000.map
INPUT_705=
INPUT_705_MAP=
INPUT_PEDIG= Example_data/example_pedigree.txt
INPUT_PHENO= Example_data/example_phenotype.txt
OUTPUT_NAME= EXAMPLEDATA
### ---------------------------------------
### --- PARAMETERS FOR plinkqc OPTION ---
### ---------------------------------------
QCMISS_IND=
QCMISS_SNP=
QCMAF=
QCHWE=
QC_OTHOPT=
### ---------------------------------------
### --- PARAMETERS FOR pedig OPTION ---
### ---------------------------------------
PDSKIPCOUPLE=
PDMEND_THRES= 0.02
PDBESTALL='N'
### --------------------------------------
### --- PARAMETERS FOR mendchk OPTION ---
### --------------------------------------
MENDERR_THRES= 0.02
### ---------------------------------------
### --- PARAMETERS FOR mds OPTION (Y/N) ---
### ---------------------------------------
MDSGROUPop='N'
### --------------------------------------------------------
### --- PARAMETERS FOR IMPUTATION - beagle3 AND beagle4 ---
### --------------------------------------------------------
BGMEMORY=
BG3_MISSING=
BG_OTHOPT=
### ---------------------------------------------------
### --- PARAMETERS FOR IMPUTATION - fimpute OPTION ---
### ---------------------------------------------------
FMP_NJOB=
FMP_OTHOPT=
### -----------------------------------------
### --- PARAMETERS FOR roh & froh OPTIONS ---
### -----------------------------------------
ROH_SNP=15
ROH_MAXMIS=1
ROH_MAXHET=1
ROH_MINLEN=1
### ----------------------------------------
### --- PARAMETERS FOR admixture OPTION ---
### ----------------------------------------
ADM_KVALUE=5
ADM_CORE=2
ADM_CV=10