Question: Which Genotype file format is it?
0
gravatar for A.Mubashir
18 days ago by
A.Mubashir 0 wrote:

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.

snp genome • 121 views
ADD COMMENTlink modified 12 days ago • written 18 days ago by A.Mubashir 0

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

ADD REPLYlink modified 12 days ago • written 12 days ago by A.Mubashir 0

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.

Is it an acceptable for further studies, such as GWAS etc.

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.

ADD REPLYlink written 12 days ago by Kevin Blighe65k
1
gravatar for Kevin Blighe
18 days ago by
Kevin Blighe65k
Kevin Blighe65k wrote:

This is not VCF.

If you would like further help, then please state the following:

  1. source of this data
  2. an example of the data
  3. what you aim to do with the data

Kevin

ADD COMMENTlink written 18 days ago by Kevin Blighe65k
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