Liftover errors with CrossMap and Picard

Question

[rshoobs]

Hi all,

I am attempting to use CrossMap to convert my dosage files output from the sanger imputation service from hg19/37 to hg38. Here is the command I am using

python3 ~/software/CrossMap-0.3.1/bin/CrossMap.py vcf ~/Data/liftover/hg19ToHg38.over.chain.gz 22_withMAF.vcf.gz ~/Data/GenCode/GRCh38.primary_assembly.fa test_output_chr22_hg38.vcf

and I receive the following error part way through

KeyError: "sequence 'b'chr22_KI270879v1_alt'' not present"

I get similar errors when I attempt to run other chromosomes. Has anyone encountered this problem before?

Additional note: I have also attempted to LiftOver using the picard LiftoverVcf tool. When I do this happens

100.0000% of variants were not successfully lifted over and written to the output

Any help that can be given towards either tool would be appreciated!

[rshoobs]

I've been trying further and find that it works with a bed file that I've created from my vcf. Only issue is that It doesn't preserve any mapping so i can't coordinate any genotypes!

[Shicheng Guo]

I have ever met the problem: sh: liftOver.hg19Tohg38: command not found, but have never met the problem you mentioned.