Hi,
Is it possible in plink to specify a non-human chromosome in the map file? I am curious if it can be run on a bacterial data set that only has 2 chromosomes and is haploid?
On the site it says:
By default, each line of the MAP file describes a single marker and must contain exactly 4 columns:
chromosome (1-22, X, Y or 0 if unplaced)
rs# or snp identifier
Genetic distance (morgans)
Base-pair position (bp units)
However, what if I just label everything chromosome 1 or 2?
Thanks!
It is not a "must" to have all chromosomes, you can run analysis on 1 chromosome if needed. But someone else should comment if Plink can be used for analysis of bacterial data.
This is true, one can use --allow-extra-chr. But whatever I try I cannot find a work-around to solve that all my .vcf do not have GT entries.