Illumina chromosome numbers 0-26 - Meaning of 0?

[LeonDK]

Hi all,

I am working on a vcf-file, where illumina has encoded the chromosomes in column as 0-26.

I have figured out, that:
1-22 autosomes
23 X
24 Y
25 XY pseudo-autosomal region
26 MT

But what does 0 signify? If I goto dbsnp and look up some of the snps from chromosome 0, they originate from different chromosomes.

[GenoMax]

See: https://www.biostars.org/p/166312/ (answer by @Robert Sicko) and https://www.biostars.org/p/102791/

[gringer]

Here are a couple of relevant points from those posts:

Chr0 probes in the genome studio project are problem probes (mapping to multiple locations, etc.) and should be omitted prior to calculating concordance

It's likely that those probes are actually control sequences used to QC the chip during development or production. It's been while since I worked with SNP chip data, but there were always a few probes that don't target human/mouse/whatever, and so those will be excluded from analysis. You should be able to distinguish them by their probe ID.

[LeonDK]

Ok, thank you.