I transformed genome coordinates from hg19 to coordinates of GRCh38 using the function liftover() from rtracklayer package in R . I used the "hg19ToHg38.over.chain" file from UCSC. But it only contains chromosome from primary assembly (ie : chr1, chr2, ..., chrY). It doesn't work for element coming from unplaced, unlocalized and alternative portions of chromosomes (for example chr6_cox_hap2, or GL000191.1, ...)
So my question is: Is there a way to find correspondance between coordinates of alternative chromosomes from hg19 and the new ones on GRCh38 ?