How to convert WGS data to microarray format?

Question

[kamanovae]

Hi!

I need to get the nucleotides corresponding to a specific chip from the WGS format. If I understand correctly, in this case it is impossible to use programs that will simply give the desired positions based on the bed file. I somehow need to consider alleles. Are there ready tools for such a task?

Thank you!

[cpad0112]

what's WGS format? In title request is for microarray format and in post, you were talking about WGS format.

[kamanovae]

Sorry, I probably didn’t formulate the question correctly. I have WGS data in bam format, but I only need to get nucleotides in specific positions in fasta/fastq format for Affymetrix chip. Can It just cut out the required positions using samtools without taking into account the alleles ?

[cpad0112]

One approach I could think of, is:

1. Subset bam with the positions of interest (using samtools view or tool of your interest)
2. Convert the new bam to fasta (using samtools fasta)

[German.M.Demidov]

I asked 2 questions about this: Deviance in allele frequencies between arrays and WGS and Genotyping: array variants from WGS - can be helpful to understand the potential problems