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I ran toil-vg construct with --force_phasing True and vg 1.20.0 when building a GBWT from a VCF set that has phase breaks (1000 Genomes on GRCh37).
--force_phasing True
The resulting GBWT did not have all contig-length haplotypes in it; there were still phase breaks.
We need to add a test for this option at a small scale, and then work out why it doesn't work (at least with construct) and fix it.
The text was updated successfully, but these errors were encountered:
Jouni says the real problem may be that we don't have a way to pass --discard-overlaps, which also causes phase breaks.
--discard-overlaps
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We also need a way to cover contigs with no VCFs with at least one GBWT thread for the primary path. I'm not sure if we do that already.
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I ran toil-vg construct with
--force_phasing True
and vg 1.20.0 when building a GBWT from a VCF set that has phase breaks (1000 Genomes on GRCh37).The resulting GBWT did not have all contig-length haplotypes in it; there were still phase breaks.
We need to add a test for this option at a small scale, and then work out why it doesn't work (at least with construct) and fix it.
The text was updated successfully, but these errors were encountered: