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When I run with unpaired reads, I get "You didn't activate --longReads, but the two files ... (which store paired-end reads) are empty - this is weird, and I will abort".
Is there support for non-p…
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Hi,
Multithread vcf filter is a great idea! Thanks for your work. I have encountered a problem while trying it. I have a vcf file produced by Stacks pipeline. I tried to filter it with `VCF_filter` b…
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Expected Behavior
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Genotyping trial would need to display uploaded files as in he field trial detail page.
For Bugs:…
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Hello, I am stuck trying to figure out why the phenotypes are not recognized in my file below. I checked that the FID/IIDs match between my pheno file and .fam file, then checked that both files are d…
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Hi Teng Gao,
I have implemented your methods on my scRNA-seq data which showed great advantages over others. I just noticed that you mentioned
'Therefore, a priori genotyping by DNA or co-genotyp…
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Hello,
Running mgatk from the venv3 environment, from the tests directory and following the instructions in the README.md, I executed:
$ mgatk call -i humanbam -o out -n glio
Tue Jul 04 13:08:24 CE…
smzt updated
11 months ago
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Dear Phil Greer,
Thanks for your help.
But I have a questions. Why is Harwin Equilibrium Analysis Not Performed During Quality Control?
Like this:
Pilnk2 --file test --hardy --out ?
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Hello,
I've encountered the following error while running a program:
The input file used is the output from minigraph-cactus.
When I created the input VCF using only 3 genome sequences, the c…
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Expected Behavior
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The same genotypes sequenced with the same genotype protocol and under the same project should have a wa…
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Hi.
I have run Manta on short-read data of 100 sample, got the union of SV sites using svimmer, and used Graphtyper2 to genotype the SVs. For some SVs there were more than one record in final VCF fi…