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lift-over-vcf's Introduction

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

lift-over-vcf's People

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Forkers

joepickrell griffan yixf-self mvelinder rduque1 alextree

lift-over-vcf's Issues

how to set output

hi can you tell me how to set output, the cmd finished in a second.
cat hapmap_3.3.hg38.vcf | python3 liftover.py --chain hg38ToHg19.over.chain.gz

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