sort order required for SNP and NOISE masks?

[gevro]

Hi, Do SNP and NOISE masks require a specific sort order of chromosomes or at all?

For example, do the chromosome in SNP and NOISE masks need to be sorted in the same order as the reference genome used for the analysis?

I noticed the supplied example SNP and NOISE masks have a different sort order (chr1, chr10, chr11, etc) than the reference genome (chr1, chr2, chr3, etc).

Thanks

[gevro]

And also, do the SNP and NOISE masks, even if they have a different sort order from the reference genome, do they have to have the same sort order?

[fa8sanger]

As far as I know none of that should matter. Any order allowing indexing should be the only thing required