I built GRM with the following commands to perform SAIGE and ran step1. The plink file is SNP data with MAF≥1% typed directly from the SNP array. The SNP data is for 1000 individuals.
#! /bin/bash
cpu=90
trait=SBP
conda activate saige
mkdir output
createSparseGRM.R \
--plinkFile=./mygeno \
--nThreads=${cpu} \
--outputPrefix=./output/sparseGRM \
--numRandomMarkerforSparseKin=2000 \
--relatednessCutoff=0.125
step1_fitNULLGLMM.R \
--plinkFile=./mygeno \
--sparseGRMFile=./output/sparseGRM_relatednessCutoff_0.125_2000_randomMarkersUsed.sparseGRM.mtx \
--sparseGRMSampleIDFile=./output/sparseGRM_relatednessCutoff_0.125_2000_randomMarkersUsed.sparseGRM.mtx.sampleIDs.txt \
--useSparseGRMtoFitNULL=TRUE \
--phenoFile=./chrs.imputed.rehead.dose.phe.txt \
--phenoCol=${trait} \
--covarColList=Sex,PC1,PC2 \
--qCovarColList=PC1,PC2 \
--sampleIDColinphenoFile=IID \
--invNormalize=TRUE \
--traitType=quantitative \
--nThreads=${cpu} \
--IsOverwriteVarianceRatioFile=TRUE \
--isCateVarianceRatio=TRUE \
--outputPrefix=./output/${trait}_sparseGRM_temo
However, after the step 1 command, I get the following error message
ERROR! number of genetic variants in 10< MAC <= 20.5 is lower than 30
Please include more markers in this MAC category in the plink file
-----------
The plink file in step 1 is required to be a hard call genotype. I used directly typed data from SNP arrays because I thought that high-quality data should be used for the step 1. On the other hand, data of low frequency SNPs in SNP array data are low quality.
I also have imputed data from same samples. The reference panel is 1000 genomes phase 3 all ancestries. This data is in vcf format, should I convert it to a plink file and use it to build the GRM and perform step 1 without the MAF filter?
I have checked the following post and have not received a clear answer to this question, so I am posting it again. I would appreciate it if you could enlighten me.
https://github.com/weizhouUMICH/SAIGE/issues/226
I built GRM with the following commands to perform SAIGE and ran step1. The plink file is SNP data with MAF≥1% typed directly from the SNP array. The SNP data is for 1000 individuals.