CrossMap liftover failed

Question

[Medhat]

I am trying to liftover HapMap.vcf dowlonaded from here for maize from AGPv3 to AGPv4 using this command;

CrossMap.py 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

Answer 1

[trentu]

Did you ever find a solution to this problem?

[Medhat]

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

[TrentGenomics]

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.