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CrossMap liftover failed

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

assembly sequencing next-gen
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updated by trentu • trentu • written by Medhat Medhat

1 answer

Did you ever find a solution to this problem?

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written by trentu • trentu

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
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written by Medhat Medhat

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.

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written by TrentGenomics • TrentGenomics

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