I've been performing liftover from hg19 to hg38 based on genetic position using the LiftOver utility. I have several snps the chromosomes of which have been labelled as such chr7_KI270803v1_alt. In particular chromosomes 7 and 8 demonstrate an inordinate amount of this tagging. On further inspection it seems like all of the positions in hg38 are significantly different from their position in hg19 (We're talking on the order of 10^7). Several are also within 1 bp of another variant in hg38, and though I haven't tested this pattern thoroughly I suspect I'd see this for many of these snps.
What's the deal with these snps? Is this peculiar chromosome tagging signifying something? Are these safe to use for further analysis or should I discard them (I'm doing eQTL analysis with MatrixEQTL among other things).
A discussion of
ALTloci can be found in this post by @finswimmer: C: Which human reference genome should I use?You can find some additional help from Ensembl about haplotypes and patches for human genome.
Information from official source at GRC.