Post by kaustubh on Sept 8, 2016 5:00:27 GMT
I am trying to run fastBAT using the instructions provided. For the --fastBAT assoc.txt file, I cut two columns of my plink assoc.linear file to create a new text file with two columns, SNP and P, including the header row. Upon running fastBAT, I get an error:
I tried including a third column containing chromosome number but then fastBAT refuses to read in the assoc file.
In the bim file I have some chromosome 0 snps, as a legacy of Illumina. Could that be a problem? The bim file had been read in properly though. Or my assoc input file is not formatted properly?
Thanks in advance.
Reading SNP association results from [/cluster/project9/gwas/eyecolor/chip_plink_short/eyecolor3.assoc.linear].
Association p-values of 674320 SNPs have been included.
Error: chromosome information is missing.
Association p-values of 674320 SNPs have been included.
Error: chromosome information is missing.
I tried including a third column containing chromosome number but then fastBAT refuses to read in the assoc file.
In the bim file I have some chromosome 0 snps, as a legacy of Illumina. Could that be a problem? The bim file had been read in properly though. Or my assoc input file is not formatted properly?
Thanks in advance.
