Questions tagged [liftover]

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How to perform liftover from 38 to 37 in R?

I have some gwas summary statistics in GRCh38 that I want to lift to GRCh37. I am trying to liftover in R using this code: ...
DN1's user avatar
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1 vote
1 answer
29 views

How important are the homozygous variants that get unnecessarily deleted using liftover?

I'm referring to the text described here: These tools [NCBI remap, CrossMap] operate only on the sites present in an input VCF, and return the representation of those sites in a new genome assembly. ...
BigMistake's user avatar
0 votes
2 answers
338 views

Lifting snp rsid build 37 to 38

I’m looking to lift over a dataset of GWAS summary stats from build 37 to 38, including converting rsid. Downstream it is to be used for co-localisation with another dataset of build 38. Would anyone ...
medicalresearcher's user avatar
1 vote
2 answers
418 views

Large amount of REF prefix differences after lifting

I lifted some unmerged trio files from hg19 to hg38 using liftOverPlink. It looks like that several houndred allels on each chromosome of one file shifted/switched to non-standard alleles. I recorded ...
mugdi's user avatar
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1 vote
3 answers
240 views

How do I lift GWAS results to hg38?

There are some questions about lifting between reference builds, e.g. this one. But there doesn't appear to be a question about lifting a GWAS results file to a new reference build (except off-site). ...
CoderGuy123's user avatar
2 votes
2 answers
1k views

Lifting from hg38 to hg37

I am having strange issues lifting this dataset to hg37 from hg38. I am using the HGDP WGS data from ftp://ngs.sanger.ac.uk/production/hgdp/hgdp_wgs.20190516/. The data set split by chromosome, so I ...
CoderGuy123's user avatar
0 votes
1 answer
415 views

Ensembl protein identifiers from different assemblies

In order to obtain orthologs for human genes, I am working with InParanoid version 7.0. This version of the database uses Ensembl Protein Identifiers (ENSP) from ENSEMBL version v54, which is based on ...
plat's user avatar
  • 1,032
2 votes
1 answer
103 views

UCSC liftover cannot produce bed format output

I was trying to use UCSC liftover tool to convert human coordinates to mouse. While most of the files worked, one file didn't: ...
Code42's user avatar
  • 282
0 votes
1 answer
171 views

What is the `table` parameter in the UCSU ldHgGene tool?

I want to lift over the annotation from E. coli release 29 to E. coli release 42. I have followed the steps for an annotation liftover mentioned here. I got the chain file for the final step and ran: ...
Biomagician's user avatar
  • 2,459
2 votes
1 answer
143 views

hgsql not found when running a script despite being accessible on command-line

I am working on macOS. I am following the steps described here to lift over an annotation from the reference genome of C. elegans to another assembly of C. elegans. I have run this code: ...
Biomagician's user avatar
  • 2,459
1 vote
1 answer
152 views

Accessing UCSC genome via ssh results in a validation error

I am working on macOS High Sierra. I am following the steps described here to lift an annotation over from one version of a genome to another. I am now just using the example genomes provided in the ...
Biomagician's user avatar
  • 2,459
8 votes
1 answer
61 views

dog coordinates (canFam3) to human coordinates (hg19)

I've converted dog coordinates to human using UCSC LiftOver. These are 200bp intergenic regions that are differentially methylated from normal dogs to cancer dogs. I've converted these to human ...
Alex Stuckel's user avatar
6 votes
3 answers
2k views

How can I compare two bed files?

I am trying to translate (lift over) bed files describing genomic regions from hg37 to hg38. I have tried both UCSC's LiftOver tool and CrossMap but saw that they give me different results. I ...
terdon's user avatar
  • 9,826
8 votes
4 answers
153 views

Working with old genome builds

Is working with and relying on old genome builds still valid? For example NCBI36/hg18. Would results from papers based on old builds require LiftOver and re-analysis to be useful? A bit of context, ...
zx8754's user avatar
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