LinkFragments in the Hapcut2 package is a python script that connects heterozygous variants based on barcode (BX) information. The way it currently does this is by connecting reads with the same BX tag that are within a certain window. This effectively re-calls the molecules we defined in buildmolecules which is quite unnecessary.
Merged PR in HapCUT2 https://github.com/vibansal/HapCUT2/pull/114 to add this functionality. Once the next HapCUT2 version is released we can update the hapcut2_linkfragments rule to use MI tags.
LinkFragments in the Hapcut2 package is a python script that connects heterozygous variants based on barcode (BX) information. The way it currently does this is by connecting reads with the same BX tag that are within a certain window. This effectively re-calls the molecules we defined in
buildmoleculeswhich is quite unnecessary.Merged PR in HapCUT2 https://github.com/vibansal/HapCUT2/pull/114 to add this functionality. Once the next HapCUT2 version is released we can update the
hapcut2_linkfragmentsrule to use MI tags.Issue copied from https://github.com/FrickTobias/BLR/issues/212