Lift-over on a VCF
6
3
Entering edit mode
9.3 years ago
win ▴ 990

Hi all,

I have a VCF file that was generated using HG18 and I want to convert it to VCF but that has HG19 data.

I am aware that there is the lift-over tool from UCSC but how do I convert a VCF file from HG18 to a VCF file to HG19, since it seems the lift-over tools produces a BED file instead.

Thanks in advance.

VCF • 23k views
ADD COMMENT
5
Entering edit mode
9.3 years ago

You may use GATK "LiftoverVariants". It allows you to use VCF file as an input and outputs a VCF file corresponding to the new assembly. Link: https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_variantutils_LiftoverVariants.php

ADD COMMENT
2
Entering edit mode

It seems that LiftoverVariants is no longer provided with GATK 3.5:

java -jar GATK/3.5/GenomeAnalysisTK.jar -T LiftoverVariants -h
##### ERROR MESSAGE: Invalid command line: Malformed walker argument: Could not find walker with name: LiftoverVariants

The link in the answer is also dead supporting the deprecation of the tool, and GATK seems to be recommending Picard LiftoverVcf.

ADD REPLY
0
Entering edit mode

Do we get the chain file from UCSC?

ADD REPLY
2
Entering edit mode

Yes, this would be a UCSC chain file.

ADD REPLY
5
Entering edit mode
6.7 years ago

Picard LiftoverVcf, which is supported by the Broad: http://broadinstitute.github.io/picard/command-line-overview.html#LiftoverVcf

ADD COMMENT
0
Entering edit mode

This worked like a charm! :) (P.S.: chromosomes in input vcf must be numerical, not preceded by "chr", and to avoid running into memory problems, use the -Xxm15G flag for the java command [if you have up to this amount of memory available]).

ADD REPLY
4
Entering edit mode
9.3 years ago

NCBI offers a remapping service (equivalent of liftover) that works with multiple formats, including VCF:

http://www.ncbi.nlm.nih.gov/genome/tools/remap

ADD COMMENT
1
Entering edit mode
6.7 years ago
yhoogstrate ▴ 150

CrossMap can do the trick as well

ADD COMMENT
0
Entering edit mode
6.3 years ago
liqigang • 0

A simple script is here, https://github.com/liqg/vcf-liftover. Using it is very simple, like this: zcat test.vcf.gz | ./vcf-liftover GRCh37_to_GRCh38.chain.gz

The converted VCF will output to stdout,you can save the unmapped variants by add a file path to store them.

ADD COMMENT
0
Entering edit mode

This hasn't worked for me: the resulting VCF was completely unstructured (but I didn't have time to investigate why this happened). Picard (as per one of the responses above) was very straightforward.

ADD REPLY
0
Entering edit mode
ADD COMMENT

Login before adding your answer.

Traffic: 2964 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6