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To better support perennial plant and animal breeders
1. Change the name "Seed Lots" to "Inventory Lots"
2. Add a "Lot Type" that can be customized by application and/or species (seed, pollen, bu…
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**1. What were you trying to do?**
Use `vg pack` to get alignment informations.
**2. What did you want to happen?**
Get the `.pack` file successfully.
**3. What actually happened?**
The p…
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Issuing the following command on a BAM file aligned against GRCh37 outputs only those SNPs located in chromosome 1:
freebayes \
--pooled-discrete \
--genotype-qualities \
--variant-input input.vcf.gz…
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The README file does not contain any version requirement for pysam, but the requirements.txt file contains the line:
pysam0.8
This is a very tight restriction and I am wondering where this is co…
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We currently do not have any functions to remove contaminated individual based on GTscore `conScore`. I propose that we create 2 functions:
- [ ] `find_ind_con` - reads in `conScore` from GTscore s…
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I am opening an issue here as I still have problems with handling variants on the X chromosome during trio analyses and would like to hear your experience about it.
1. Phase by Transmission is not plo…
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Hello,
We have a dataset of SVs created from PacBio data using pbsv. We'd like to take those SVs and use delly to genotype a dataset of Illumina WGS samples at these specific sites. We made a sites…
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Expected Behavior
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As requested by Prasad
Submission 18 DArTseqLD: [https://www.dropbox.com/t/7rRmj0FjRlDJYGKH](https:…
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Qualimap needs an `ext.prefix`.
Additionally, Qualimap results are meant to be at the sample level, but are currently at the Library level. We need to use post-Library-merge BAMs as input for this …
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comma or tab separated? how about pairwise sequencing?
can I use compressed files, like gz or tar.gz?
here is an example of my manifest.tsv, is this ok?
########################################…