Errors using liftOver

[Gottlieb, Assaf]

Hello,

I am trying to use liftOver to map a GWAS study in bed format from build 36 (hg18) to build 37 (hg19). I have not succeeded in using liftOver and need assistance:

1.       The online tool doesn’t work for me. I upload the bed file but after I hit submit, it seems to upload the file but nothing happens afterwards (tried two different browsers).

2.       I tried using the linux version. The first thing I noticed is that there is no hg18ToHg19.over.chain file, only hg19ToHg18.over.chain at http://hgdownload.soe.ucsc.edu/goldenPath/hg19/liftOver/ . Will that work?

3.       Even if I try to use hg19ToHg18.over.chain with the following command
>./liftOver data_file_hg18.bed hg19ToHg18.over.chain data_file_hg19.bed unMapped.txt
I get the following error:

Reading liftover chains

Mapping coordinates

Expecting integer field 2 line 1 of LOAD-610K_FORWARD_strand_consent_1.bed, got ��������?���������

Which tells me it was expecting a text file and not binary?

 

 

Kind Regards,

Assaf

 

-----------------

Assaf Gottlieb

Assistant Professor, Center for Precision Health

School of Biomedical Informatics

The University of Texas Health Science Center at Houston

7000 Fannin St. Houston, TX 77030

Phone: 713-500-3698

 

[Conner Powell]

Dear Assaf,

Thank you for using the UCSC Genome Browser and for your question about the liftOver tool.

We were unable to reproduce your error on either the online liftOver tool or the command line liftOver tool. Based on the error message you received:

'Expecting integer field 2 line 1 of LOAD-610K_FORWARD_strand_consent_1.bed, got ��������?���������'

It appears there may be a conflict with the value used in field 2, which should contain the chromStart value. We recommend verifying that your input .bed file is in proper BED format. To read more about BED format, you can use the following link: https://genome.ucsc.edu/FAQ/FAQformat.html#format1. If you continue having issues after you have verified that the file is in BED format, you can send it to us for further debugging. If your file contains private data, you can send it to use offlist at: genom...@soe.ucsc.edu.

Additionally, the liftOver chain file between two assemblies is always in the 'liftOver' directory for the starting/query assembly, e.g hg18 in this case. The hg18ToHg19.over.chain file can be found in the hg18/liftOver directory: http://hgdownload.soe.ucsc.edu/goldenPath/hg18/liftOver/hg18ToHg19.over.chain.gz

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Conner Powell

UCSC Genomics Institute, Quality Assurance and Support Analyst 

[Conner Powell]

Dear Assaf,

Thank you again for using the UCSC Genome Browser and for your follow-up question about liftOver.

Could you please elaborate on what tool you used for flipping the strands? Also, it may be helpful to contact the author of the tool you used to troubleshoot the error you are receiving.

Additionally, if the genotypes you are using can be converted to VCF format(https://genome.ucsc.edu/FAQ/FAQformat.html#format10.1), then the tool CrossMap might be able to both liftOver and adjust strands/alleles. Here is a link to the CrossMap documentation page: http://crossmap.sourceforge.net/

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

On Tue, Mar 5, 2019 at 7:32 AM Gottlieb, Assaf <Assaf.G...@uth.tmc.edu> wrote:

Hello Conner,

Thanks for your reply. It made me realize the difference between UCSC and plink BED files. As a follow-up – I managed to liftover an hg18 to hg19 version. I proceeded to use another tool for flipping the strands as I did for other genotypes that did not need lifting. However, upon trying to impute, I still have errors regarding erroneous strands.

What is the correct procedure to both liftOver and flip strands? Should I only liftOver or flip before the liftOver?

 

Regards,

Assaf