ligateHaplotypes/equivalent in shapeit 4

[hardingnj]

Hi there,

When using region shapeit2 came with the functionality to "stitch" the outputs from different regions together into a single scaffold.

Although shapeit4 has the same region flag- I don't see a mention of postprocessing these chunked outputs in the docs. Is this still possible/supported?

many thanks Nick

[odelaneau]

Dear Nick,

Please do have a look at:

bcftools concat with option --ligate

http://www.htslib.org/doc/bcftools.html#concat

Hope that helps;

Olivier

[hardingnj]

many thanks!