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-- genotyping protocols have overlapping markers and filtering for shared markers among protocols allows including accessions genotyped using different protocols in analyses pipelines. (request from M…
isaak updated
2 years ago
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Provide a workflow to force genotyping for all variants provided in an input VCF. For example, apply the manta candidate output from a joint trio analysis to additional family members.
Adding: @holtg…
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Plural forms should be used instead of singular (to be consistent):
- BrAPI-Genotyping > Variant Sets > /variantsets/{variantSetDbId}/variants
(array) variantSetDbId --> variantSetDbIds
- BrA…
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I have a dataset that I am trying to convert to gtc but ran in to an error using bcftools and idat2gtc version 1.20. GEO accession is GSM5579064 and an example that works on the same dataset GSM557906…
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Hello,
Wondering if it's possible to build indexes for quick genotyping of low coverage samples ( ~2-5x ~1500+) from a set of samples generated at higher coverage (~500, 10-20x) for a fish species …
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### Description of the bug
Hi, I have added path for multiple vcfs inside samplesheet.csv as input to the pipeline and kept `chr` column empty as recommended ("If the target genomic data file conta…
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Dear LUSH Team,
Can the GenomicDB workspace be used as input for the LUSH_GenotypeGVCFs module instead of a combined multi-sample GVCF?
Best Regards,
Anurag
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Once the name/ID clean-up is done, entries whose names still have "tools" or "websuite" (and maybe other things) should gain the annotation toolType==Suite
e.g.
https://bio.tools/tool/Virus_Genot…
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Hi,
```
version: v3.0.1
Files and parameters used:
-e 3000000000
-k 31
-o index/processed
-r chm13v2.0.fa
-t 10
-v merged.sorted.multi.vcf
Determine allele se…
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I am running phase_common on a BCF file (as well as variants to exclude in another BCF) acquired from an Axiom array.
While running, it gives an error stating that `AC field is needed in file` for …