Question: unplaced, unlocalized, ... scaffolds from hg19 to GRCh38
gravatar for tabone.olivier
5.2 years ago by
tabone.olivier10 wrote:

Dear all,

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 ?

Thank you,


assembly • 2.4k views
ADD COMMENTlink modified 5.2 years ago • written 5.2 years ago by tabone.olivier10

as far as I know these elements do not exist anymore in hg38.

ADD REPLYlink written 5.2 years ago by Giovanni M Dall'Olio27k

Thank you for your answer. Ok they don't exist but i am still surprised there is no correspondance between unlocalized scaffolds (known chromosome, but unknown position within chromosome) from hg19 and the "good" position within chromosome in hg38.

ADD REPLYlink modified 14 months ago by Ram32k • written 5.2 years ago by tabone.olivier10

Was this resolved somewhere else besides this post? I am having the same issue but for lifting over variants ("LiftoverVcf Encountered a contig, 2_KI270773v1_alt that is not part of the target reference."). I am using the latest version of Picard, and the proper liftover file. Is the best way forward to just drop the hg19 variants that are on these contigs that are not part of hg38? Any help on this would be appreciated.

ADD REPLYlink written 8 months ago by brismiller40
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