Stark
New Member
Posts: 6
|
Post by Stark on May 22, 2017 3:06:31 GMT
Hi,I have some question about GCTA-fastBAT?Is Anybody can help me?
Qestion1:Is the GCTA-fastBAT can only used in human data? Can I use GCTA-fastBAT in other species?
Question2:About the input data file of GCTA-fastBAT,the SNPs in assoc.txt must be rs IDs? Can I use the SNP names(eg.ARS-BFGL-NGS-90407) in input file? And is gene position in the gene_list.txt must be match with the SNP position? And when I use the GCTA-fastBAT it doesnot show any output. Options:
--bfile qc
--autosome-num 30
--fastBAT glm.txt
--fastBAT-gene-list gene_ensembl.txt
--out glm_fast
Note: This is a multi-thread program. You could specify the number of threads by the --thread-num option to speed up the computation if there are multiple processors in your machine.
Reading PLINK FAM file from [qc.fam].
individuals to be included from [qc.fam].
Reading PLINK BIM file from [qc.bim].
44046 SNPs to be included from [qc.bim].
Reading PLINK BED file from [qc.bed] in SNP-major format ...
Genotype data for 2592 individuals and 44046 SNPs to be included from [qc.bed].
Reading SNP association results from [glm.txt].
Association p-values of 44046 SNPs have been included.
Analysis finished: Mon May 22 10:23:47 2017
Computational time: 0:0:2
Thanks in advance for any help,
Stark
|
|
|
Post by Jian Yang on May 24, 2017 14:28:10 GMT
Re 1) Yes
Re 2) It doesn't have to be rsID but needs to be consistent with the ID in the PLINK files (--bfile).
|
|