possible to convert hg19 coordinated position to hg38 coordinated position??

Question

[hs960201]

hi i'm just beginned graduate school student i have bunch of panel of normal files that made by lab predecessor(senior) who already graduated and those are hg19 coordinated. the looks like this :

#CHROM   POS   REF   ALT   DPsum;DPn;VARsum;VARn;VAFpct
1       10003   A    AC       4166;36;6;6;0.14
......

but nowadays quite many tools support hg38 and tools like Mutect2 they highly recommend using hg38 reference so i wanna change my hg19 coordinated PON file to hg38 coordinated PON file if it's possible but i can't find appropriate way i don't have any BAM or fastq file that used for PON but i really need it for VCF post filtering thanks for in advance for any reply

Answer 1

[Sam]

What you are looking for is LiftOver

[hs960201]

Thanks for reply. i tried it yesterday with Crossmap.py but there were some unmaped region about ~2% of total VCF called region how can i handle this unmapped region? could be manually liftover it but it's gonna be real labor-intensive work. is there any solution for it?

thanks you for reply again.

[Sam]

I've never used Crossmap and have alway used LiftOver. However, it is normal to have regions that you cannot lift. You can try running LiftOver and see if you have similar level of unmapped region. Otherwise, I am not aware of any other method that can perform a 100% liftover.

[hs960201]

hi sam thank you for rapid reply OK i'm gonna try LiftOver and nevertheless if they can not map that unmapped in Crossover.py results it's worth to try manually liftover for some variants

thanks have a good day