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Hello,
thank you for your efforts in providing this tool.
I have a question that I could not solve from the extensive documentation and thought maybe you could help me out.
My use case:
I hav…
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## Problem
I am getting a `ValueError: data must be 2 dimensions` when running LinkedSV (see below for full error message & context).
## Possible solution
I am running this on data which is …
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Hi Colin
This is Paolo once again.
I think there is still some problem with the sign in hapbin 1.3 for the calculation of the iHS.
Based on my understanding the iHS value of a SNP should be log(iHH…
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Hi Brad,
We're almost there when it comes to integrating the new vep. I'm still having some issues though. I think those are mainly because we use an uncompressed fasta as reference for the HGVS no…
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Hi there,
Thanks so much for posting this package - I am very excited to use it on my single cell data. I have been trying to configure Chisel on our cluster since your 10x Webinar, however I am ru…
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Is there an option to run freebayes with the `--pooled-continuous` option, and if not, would it be doable/easy to add in a newer version?
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I have created a collapsed assembly using Canu (https://github.com/marbl/canu) and now would like to run HAPCUT2 for phasing. Is there a recipe or code for this. Thank you.
> From Canu
> Smash hap…
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## Bug Report
DavidR says to bring this to your attention @yfarjoun.
### Affected tool(s)
CrosscheckFingerprints called from GATK4.0.4.0
### Affected version(s)
- [x] Latest public release ve…
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We are starting to look at paired sequencing data and I am starting to wonder how one determines uniqueness of a pair of sequences. This is related to #246 but I thought it worthy of a separate discus…
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I was wondering if how DeepVariant performs on short tandem repeats and small inversions has been characterized?
I imagine small inversions aren't a problem, but short tandem repeats might be.
…