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3.6 years ago
Abbas.M
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Chromosome Position RefBase AltBase MAF RefBaseNum AltBaseNum Sample 1 Sample2 Sample3
I am confused about this format. I have downloaded it from an online database. I looks like vcf format, but it is not supported by any software.
Thank you so much for your quick response. However, i answered very late, and sorry for that. I read a lot of stuff and figure out that the genotype file that i have, doesnot follow any format. Actually, it is neither vcf nor any other format. I have converted it in hapmap, vcf and plink format. Another question that i want to ask about the single bit coding of SNP and double bit coding such A is single and BB is double bit coding. The orginal genotype file that i have, was in double bit coding and when i converted it in hapmap format from tassel, it became single bit. I mean, in the converted HapMap file, the SNP are coded as single, like N, A and so on. Is it an acceptable for further studies, such as GWAS etc. I read some literature, in which they mentioned both coding systems are acceptable. I have a large data set of plant for salt treatment and hormone treatment. Control and treatment files are separate. Now, I want to do GWAS on it. Since, i am new to GWAS, so i am confused , whether i need to do GWAS on control and treatment data separately. Kindly, explain it in detail? Do i need to do GWAS on control and treatment data separately. If so, then how to compare the GWAS results of both control and treatment?.Thanks
Hi, I cannot possibly explain all 'quirks' of GWAS in a single reply. I may suggest that you do further reading to figure out which program you want to use.
It depends on which program you want to use. I am not even sure to what, exactly, you mean by single- and double-bit (?). 'A' and 'B' allele encodings are inconsistent and not standardised.