Post by dianacornejo on Sept 2, 2020 15:44:19 GMT
Hello,
I am really confused about FastGWA output
In the documentation I found that the output is as follows:
Output format
test.fastGWA (columns are chromosome, SNP, SNP position, the effect allele, the other allele, per allele sample size, frequency of A1, SNP effect, SE and p-value)
However, I'm having difficulty to understand what the effecte allele refers to (I would expect it to be the minor allele). However when I look at my output
I'm finding that is not the case since most of the A1F are above 0.5. As input I'm using the bgen files from the UK Biobank data which format is REF/ALT alleles.
I would like more clarification on how FsatGWA is using that inputed data and if there is a possibility to change the output to show the effect allele as the minor allele.
Thanks in advance
I am really confused about FastGWA output
In the documentation I found that the output is as follows:
Output format
test.fastGWA (columns are chromosome, SNP, SNP position, the effect allele, the other allele, per allele sample size, frequency of A1, SNP effect, SE and p-value)
However, I'm having difficulty to understand what the effecte allele refers to (I would expect it to be the minor allele). However when I look at my output
I'm finding that is not the case since most of the A1F are above 0.5. As input I'm using the bgen files from the UK Biobank data which format is REF/ALT alleles.
I would like more clarification on how FsatGWA is using that inputed data and if there is a possibility to change the output to show the effect allele as the minor allele.
Thanks in advance