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8 votes
Accepted

Working with old genome builds

In my opinion, it is not very reliable. LiftOver is very limited in terms of transformations it can support. The LiftOver Chain format can capture only matching regions in the same order. It means ...
Karel Břinda's user avatar
4 votes

Ensembl protein identifiers from different assemblies

Those IDs are elderly! Ensembl 54 was 2009! I would recommend using BioMart combined with the ID history converter. The ID history converter will convert old IDs to new, and BioMart will convert ...
Emily_Ensembl's user avatar
4 votes

Working with old genome builds

I think that right now, the only human builds that are worth considering are hg19/GRCh37 as many data bases such as gnomAD still exclusively use this release. On the other hand, hg38/GRCh8 has many ...
Manuel's user avatar
  • 588
3 votes

How do I lift GWAS results to hg38?

Yes. LiftOver tools, if they work on VCF data (some only take BED as input) work on GWAS summary statistics. You could use https://pypi.org/project/liftover/, for example.
BigMistake's user avatar
3 votes
Accepted

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

I stumbled across this issue after getting the same warning message from liftOver. By using the -out option of ...
knowah's user avatar
  • 46
3 votes

How can I compare two bed files?

From a set operations viewpoint, consider your hg37 regions as a "reference" set and hg38 as a "map" set. If you have these sets in BED format, BEDOPS lets you do set operations on them with various ...
Alex Reynolds's user avatar
2 votes

How can I compare two bed files?

I wrote ParsEval to handle these types of comparisons. ParsEval reports a variety of similarity statistics at both the nucleotide level and feature (exon) level. It doesn't explicitly support "fuzzy" ...
Daniel Standage's user avatar
2 votes

Working with old genome builds

You could use liftOver which isn't always great. Whenever I encounter this (especially NGS data readily available on the SRA), I often just get the raw files (e.g. fastqs) and re-align/re-map. In ...
story's user avatar
  • 1,573
2 votes
Accepted

Accessing UCSC genome via ssh results in a validation error

You need to setup ssh keys. All the commands in the script are going to use ssh to run the commands. Note the tips here of how to setup ssh keys: http://genomewiki.ucsc.edu/index.php/...
Null Model's user avatar
2 votes

How do I lift GWAS results to hg38?

I would advise against using dbSNP rsIDs to perform a liftover as they get updated over time. I recently wrote a software to liftover summary statistics and the documentation includes instructions ...
Giulio Genovese's user avatar
2 votes

How do I lift GWAS results to hg38?

It turned out to be easier than expected. You figure out which dbSNP version they used. dbSNP is the classification system for snps based on the rsid format. Pretty much every GWAS publishes their ...
CoderGuy123's user avatar
2 votes
Accepted

Lifting from hg38 to hg37

BED format can refer to the ".txt" file format that stores chromosomes and positions of genomic features as well as some other things like name. bed ...
Phoenix Mu's user avatar
2 votes

How to perform liftover from 38 to 37 in R?

Thanks for your post, I tried your code in R with my GwasSumstats with some adjustments from https://bioconductor.org/packages/release/workflows/vignettes/liftOver/inst/doc/liftov.html and it works. ...
Eleanor's user avatar
  • 21
2 votes

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

All this is saying is that the tool doesn't lift over variants which aren't present in the vcf. I can't imagine this being a big deal in any analysis I've done and it's exactly what I'd expect the ...
user438383's user avatar
  • 1,689
1 vote

Liftover variants/vcf called on NCBI reference genome

Could you use the hg19 --> hg38 chain from here? As I understand it, the main difference between GrCH37 and hg19 are the format the chromosomes are written (whether there is a "chr" ...
Sarah's user avatar
  • 516
1 vote

Liftover variants/vcf called on NCBI reference genome

Liftover is hard. While many variants can be lifted over relatively easily, some cannot. First, some variants are not even variants in the other genome (the other genome has the variant allele as the ...
terdon's user avatar
  • 10.2k
1 vote
Accepted

UCSC liftover cannot produce bed format output

I figured out the issue by myself. It turned out that UCSC liftover doesn't like the character ":" I removed ":" and it worked
Code42's user avatar
  • 282
1 vote

Lifting snp rsid build 37 to 38

There are multiple tools to use for this. Might I suggest the following reads: Introduction to liftover tools, where they also refer to this usefull post BioStars post. Maybe also consider reading ...
Dandelion's user avatar
  • 313
1 vote
Accepted

Large amount of REF prefix differences after lifting

It is important that after lifting over a VCF/BCF file from one coordinate system to another, the header of the resulting file contains the chromosome/contig names as present in the coordinate system ...
JRodrigoF's user avatar
  • 827
1 vote

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

It is possible that the shell being used in the process is different from your standard command line shell. I am not familiar with the tool, and it's hard to say more without knowing your OSX version, ...
Maximilian Press's user avatar
1 vote

dog coordinates (canFam3) to human coordinates (hg19)

Based on this old answer, this is not recommended for liftOver. For between-species liftovers, it is claimed that you are likely to want a different tool such as pslMap. For a lot of rather detailed ...
Maximilian Press's user avatar

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