lift-over-vcf

UCSC liftOver (genome build converter) for vcf format

Usage example

E.g., Convert 1000 Genomes (build 37) to build 38:

$ cat ${vcf}| python lift-over.py --chain hg19ToHg38

filename in test/data	description
ALL.chr15.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf	1000 Genomes data from FTP
ALL.chr15.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.liftover_to_b38.vcf	+ lift over from b38

E.g., Convert HapMap (build 36) to build 37:

$ cat ${vcf}| python lift-over.py --chain hg18ToHg19

filename in test/data	description
genotypes_chr12_JPT+CHB_r24_nr.b36_fwd.txt	HapMap genotype data from FTP
genotypes_chr12_JPT+CHB_r24_nr.b36_fwd.txt.vcf	+ convert to vcf
genotypes_chr12_JPT+CHB_r24_nr.b36_fwd.txt.liftover_to_b37.vcf	+ lift over from b37