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running:
set -o pipefail; /usr/local/bin/gemini load --passonly --skip-cadd --skip-gerp-bp -v /mnt/work/freebayes/50T-effects-ploidyfix-filter.vcf.gz -t snpEff --cores 1 --tempdir /mnt/work/freeba…
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Hi hatchet developers:
I ran " python3 -m hatchet run hatchet.ini", it created "snps" folder in "output", then the error occured below, how to fix it?
Thanks,
Wei
The step "phase_snps" req…
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Open Targets' locus to gene (l2g) prediction can inform VEP users if a queried variant is part of a GWAS loci and if that loci can be linked to a gene.
**The scope of this ticket includes**:
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Hi,
a user mailed and asked whether we could implement genosets - collections of SNPs and their alleles which together are linked to a certain disease/phenotype.
For example, gs181 has rs1135840(G)…
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In https://github.com/phetsims/energy-forms-and-changes/issues/216 we discussed a new feature which would show a user interface for selecting query parameters for the simulation.
From the notes, …
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Hello,
I am trying to set specific genotypes to missing using bcftools +setGT on a multi-sample vcf. I believe there have been similar bugs reported for this plugin. Would it be possible to help f…
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Hello!
We found some unexpected behaviour in the PyBSAseq script. When setting a window size that is too small, meaning that there are windows that do not contain any SNPs, PyBSAseq fails with the …
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Hello,
I would like to use whatshap polyphase for some samples with ploidy 3. I am using sequence data from Nanopore. The problem is that for SNP calling, the variant callers specific to Nanopore d…
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Currently, the data model for container types (Datasets, VariantSets and ReadGroupSets) in the GA4GH API is vague and ill defined. Where definitions are given, they refer back to the data file format…
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Working with several different sequencing runs of various qualities I am trying to develop intuition for what reasonable quality filtration parameters are in the function `filterAndTrim`. The relevant…