I have some genetic data in a bim file.
The chromosomes range from 0 to 23 and 26, which I have not come across before. Would the SNPs on chromosome 0 and 26 be removed from the genetic file or left in. Then, I have some SNPs which have a GSA (which the genotyping array) before the rsid but some appear normal without the GSA prefix, see below
19 GSA-rs117797881 88.57582 51991438 G A
19 rs7259137 88.47165 51972314 G A
The SNPs on chr 26 look like this
26 MTReverseDLOOP_61 100 16399 G A
I am tempted to remake the file including only chromosomes 1-23 and removing the GSA prefix as the position and chromosome align with the correct SNP identifier (Hg38). Would leaving the Chromosome 26 in have any impact on imputation?
Would really appreciate advice/reassurance.