Hello!
I have issues finding what CHR_HG126_PATCH or CHR_HSCHR19KIR_T7526_A_HAP_CTG3_1 stand for. I have tons of names like that in my Chromosome.scaffoldname variable among normal (1, 23) chromosome names. I thought at first it might be mitochondrial but now I'm not so sure... Thanks!
Unfortunately, when the Genome Reference Consortium (GRC) releases a new reference genome, one would think that its sequence is 'pristine', representative of the global population, and will remain fixed over time. This however, is far from the truth. For an intro into what I'm alluding, see my answer here: A: Alternate nucleotide is more frequent than reference nucleotide. OMG I'm dizzy.
The patches are updates to a pre-existing released reference genome. This can mean fixing sequence that was already released or adding on new sequence that was not originally included. These are explained by the GRC - I will just post the link:
These particular patches are for GRCh38 - you can see all other GRCh38 patches here:
From where did you obtain your data and which original genome was used for alignment? As the analyst, you can make an 'executive' decision about how to manage these. It can be that you have data-points listed twice, one for the original chromosomal contig, and one for the patch covering that same contig.
Kevin
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