gretel

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Hi! I am hoping to use Gretel to retrieve haplotypes from a set of BAM files. When I run Gretel, though, I get the following error: ``` [None] [NOTE] Loaded...

Saannah

Huge temporary files when running gretel on very large contigs

7

Although Gretel is not designed for recovering large haplotypes, it should at least try its best. Apparently very large contigs will cause Gretel to write very large temporary files and...

SamStudio8

The docs website points to the old `snpper` script in the testing repository (which should perhaps be removed or archived given its age), rather than showing an invocation of `gretel-snpper`....

SamStudio8

Improve error message for no bridge found

7

Hi, I run Gretel on different datasets. I've got this error message : > [FAIL] Unable to recover pairwise evidence concerning SNP #15 at position 1077 Gretel needs every SNP...

jsgounot

Non-compressed VCF should emit warning (or just drop pyVCF)

1

SamStudio8

[tracking] Ideas for future work

3

* [ ] Attempt to "ramp" the start of the target region by decreasing -s automatically * [ ] Minimal marginal aware reweighting * [ ] Reconsider approach for minimal...

SamStudio8

SamStudio8

Insert detected insertions onto the reference

1

SamStudio8

Find a happy system for reweighting

2

Currently, reweighting works pretty well, apart from cases like this:  We end up "spending" the observed GA's on the first few rounds of path finding. Leaving...

SamStudio8

SamStudio8