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odelaneau / GLIMPSE

Low Coverage Calling of Genotypes
MIT License
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Reported phasing (GT field) #177

Open srubinacci opened 11 months ago

srubinacci commented 11 months ago

[GLIMPSE2] Potential bug in the reported phased genotypes (GT field). Should be fixed in the testing version and will be updated in the new release as soon as possible.

srubinacci commented 11 months ago

For haplotype analysis, best option is to rephase the data with shapeit (phase_common with ref. panel) for now.

srubinacci commented 5 months ago

Commit: f310862ad6619e751d5b7f0590a940f3983a7602

Solves part of the problem during ligation step - wrong use of htslib caused no switch.

Thecover commented 3 weeks ago

Hi,

I am very interested in using GLIMPSE2. I have encountered an issue when using vcf or bcf files as input for the GLIMPSE2_phase step. Due to a bug, the process fails with a "Segmentation fault" error. I suspect this might be related to the issue mentioned in this GitHub issue, which prevents the use of vcf files as input. Could you please provide any insights or solutions to this problem?

Thank you!