Question: CrossMap liftover failed
gravatar for Medhat
3.8 years ago by
Medhat8.8k wrote:

I am trying to liftover HapMap.vcf dowlonaded from here for maize from AGPv3 to AGPv4 using this command; vcf AGPv3_to_AGPv4.chain.gz all_chr_hmp321_withDPGL_imputed.vcf.gz genome_AGPv4.fa ./all_chr_hmp321_withDPGL_imputed_AGPv4.vcf

but Total entries number equals Failed to map number (meaning it did not liftover any)

Read chain_file:  AGPv3_to_AGPv4.chain.gz  
Creating index for genome.fa  
Total entries: 8315314  
Failed to map: 83153144  

my chain downloaded from here

help is appreciated

sequencing next-gen assembly • 2.1k views
ADD COMMENTlink modified 3.1 years ago by trentu0 • written 3.8 years ago by Medhat8.8k
gravatar for trentu
3.1 years ago by
trentu0 wrote:

Did you ever find a solution to this problem?

ADD COMMENTlink written 3.1 years ago by trentu0

Yes: I chose different software and the result was good.

java -jar picard-tools-1.100/picard.jar LiftoverVcf I=input.vcf.gz O=output.vcf CHAIN=AGPv3_to_AGPv4.chain.gz REJECT=rejected.vcf R=genome.fa 2>&1  ./out.log
ADD REPLYlink written 3.1 years ago by Medhat8.8k

Thanks Medhat, I'll give that a try as well. I ran into the same problem where my number of map fails was equal to total entries.

May I ask what program you used to generate your chain file, or did you download one?

Thanks again.

ADD REPLYlink written 3.1 years ago by TrentGenomics30
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 905 users visited in the last hour