diff --git a/README.md b/README.md index 4957087..3769b0d 100644 --- a/README.md +++ b/README.md @@ -11,11 +11,12 @@ Dependencies: * Python 3 (tested on version 3.6.9) * [gramtools](https://github.com/iqbal-lab-org/gramtools) commit 9313eceb606a6fc159e4a14c168b7a6f888c5ed2 +* [bcftools](https://samtools.github.io/bcftools/) * [vt](https://github.com/atks/vt.git) * [vcflib](https://github.com/vcflib/vcflib.git). Specifically, either `vcflib`, or all three of `vcfbreakmulti`, `vcfallelicprimitives`, and `vcfuniq` must be installed. -* Optionally, [nextflow](https://www.nextflow.io/), if you want to use the +* Optionally, [nextflow](https://www.nextflow.io/) and [ivcfmerge](https://github.com/iqbal-lab-org/ivcfmerge) if you want to use the pipeline to regenotype a large number of samples. Install by cloning this repository (or downloading the latest release), and