Does bcftools support any kind of large dictionary based editing of variants?

Question

[rshoobs]

I have a text file of snp positions that change between builds and would like to update my vcf file accordingly. I could throw the whole thing into R, but I'd like to know if bcftools has anything more convenient. Essentially I am looking for something that interfaces with the output of liftOver in a convenient way.

Answer 1

[Pierre Lindenbaum]

liftovervcf https://software.broadinstitute.org/gatk/documentation/tooldocs/4.0.0.0/picard_vcf_LiftoverVcf.php