diff --git a/README.md b/README.md index 55556f6f44d..1769d290e59 100644 --- a/README.md +++ b/README.md @@ -396,14 +396,6 @@ vg index hla.vg -x hla.xg vg deconstruct hla.xg -e -p "gi|568815592:29791752-29792749" > hla_variants.vcf ``` -Variants can also be inferred strictly from topology by not using `-e`, though unlike the above example, cycles are not supported. "Deconstruct" the VCF variants that were used to construct the graph. The output will be similar but identical to `small/x.vcf.gz` as `vg construct` can add edges between adjacent alts and/or do some normalization: - - -```sh -# using the same graph from the `map` example -vg deconstruct x.xg -p x > x.vcf -``` - Haplotype paths from `.gbz` or `.gbwt` indexes input can be considered using `-z` and `-g', respectively. As with `vg call`, it is best to compute snarls separately and pass them in with `-r` when working with large graphs.