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For first round of integration testing with Kids First, we need the priority 1 fields from sequencing (and maybe 2). These fields include:
### Priority 1
seq_filename
analyte_type
sequencing_…
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Hello, I am trying to generate the input for SIGNALS using hmmcopy and counthaps; we have single-end data and we have realized that our data doesn't work with your software, specifically for the count…
shngk updated
5 months ago
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Hi,
I m trying to impute HLA in TopMed Imputed data using Michigan Imputation Server. However job fails stating "**Calculating QC Statistics failed**". Also, when I try to impute Michigan Server Impu…
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Would it be possible to handle ambiguous reference bases properly? That would increase the alignment quality for viral use cases.
Thank you.
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Hi @cdarby
Thanks for making this tool! I'm having some trouble interpreting the outputs, and I'm hoping you can help.
So I've run the pipeline twice now on two different 3' scRNA-seq PBMC data…
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Hello,
I'm trying to use Graphtyper as it seems to be fast and to scale well to many samples. Very easy to install and run so far.. but I'm unsure that I'll be able to make the most of it.
My unde…
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Could someone help me package GATK 4.4.0.0? Here is what my package definition looks like thus far:
```
(define-public gatk
(package
(name "gatk")
(version "4.4.0.0")
(source (or…
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I had originally posted this in guix-science-nonfree where it was brought to my attention that GATK is now free software. I have been having a bit of trouble packaging it and would appreciate help fro…
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HaplotypeCaller
Call germline SNPs and indels via local re-assembly of haplotypes
Overview
The HaplotypeCaller is capable of calling SNPs and indels simultaneously via local de-novo assembly of haplot…
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Hello, team.
First I want to say thanks to this nice tool.
Other functions in this tool work good like _genotype_. in my single cell RNA sequencing data (+single end).
I downloaded this tool f…