Issues when using liftOver to convert hg19 to hg38

[Ruyu Shi]

Hi, I downloaded the liftOver linux version and the hg19ToHg38.over.chain.gz file from https://genome-store.ucsc.edu/products/. I am trying to run the program on the server. 

The command I used is pasted below: 

1) to prepare the bed format file as input:

awk '{print $1 "\t" $4-1 "\t" $4 "\t" $2 "\t.\t."}' All_Cohorts_Case_Control_filtered.bim > All_Cohorts_Case_Control_filtered_GRCh37.bed

2) to activate the liftOver tool:

chmod +x ../../tools/liftOver

3) to run the program:

../../tools/liftOver All_Cohorts_Case_Control_filtered_GRCh37.bed ../../tools/hg19ToHg38.over.chain.gz All_Cohorts_Case_Control_filtered_GRCh38.bed unlifted.bed

However, I have no valid output. The unlifted.bed file shows #Deleted in new for all variants. I am not sure why this is happening. Can you please give me some suggestions on modifying the commands? I appreciate your help. 

The header of the input .bed file looks like the screenshot attached in this message.

Best,

Ruyu

[Gerardo Perez]

Hello, Ruyu.

Thank you for your interest in the Genome Browser and for your question about liftOver.

Looking at the screenshot, it looks like the bed file has NCBI chromosome names (chromosome 1 = “1”) whereas the liftOver utility requires bed format in which the chromosome names are UCSC convention chromosome names (chromosome 1 = “chr1”). You can slightly modify your command to the following to change the chromosome names as UCSC convention chromosome names:

awk '{print "chr" $1 "\t" $4-1 "\t" $4 "\t" $2 "\t.\t."}' All_Cohorts_Case_Control_filtered.bim > All_Cohorts_Case_Control_filtered_GRCh37.bed

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 Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute

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