Na (No Value) In Chromosome In Output Snp Test

Question

[Martijn]

For GWAS, I am using SNP Test 2.4 and/or 2.5.

I built this in a pipeline.

SNP Test works fine, but there is one problem: There is no output of the chromosomes generated in the SNP Test. At all SNPs in the SNP Test output, NA is given at all the chromosome.

What is/can be the cause of that?

Answer 1

[mirko.treccani01]

Hi!

If you mean that the chromosome column presents only "NA" value, just use the -assume_chromosome option before running the command.

snptest -assume_chromosome # -data *.gen *.sample [etc.] where # indicates the number of the chromosome.