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Hello! I am interested in calculating aFC for genes with multiple causal variants and was pointed to this tool by Stephane Castel.
This seems like a really great extension of the aFC tool! I was cu…
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I have a set of 4 exomes and running aldy 4.4 on them as so:
aldy genotype -g cyp2e1 -p wxs ${bam_location}/*/${sample_name}.bam -o ${output}/${sample_name}.cyp2d6.aldy -l ${output}/${sample_name}…
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Hi,
Thank you for sharing this tool with the community. After reading the manual and issues, I would like to use LongPhase for my genome projects.
FYI,
Input data: PacBio (Sequel) with ~200X c…
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Would it be possible to add "Seed" to the tissue type drop down menu for genotyping plates? Alternatively it might be nice to add tissue_type as a configurable key option.
ch728 updated
10 months ago
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Hi,
I started a new issue as I am not sure on how the short reads should be handled and others may also be interested in the answer.
1) It says that the reads should be "Paired-end reads must be…
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**1. What were you trying to do?**
mapping short reads to and call SVs from reference + vcf graph.
**2. What did you want to happen?**
vg call produce vcf file with SVs called.
**3. What ac…
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Is there a way (or would be difficult) to output a BAM with the reads that contributed to the SV calls, with a SAM tag that identifies which call? This is super useful for debugging calls in IGV. Fo…
nh13 updated
10 months ago
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I have constructed two CSV files, which are processed with two different sets of resequencing data against the same REF.
However, when I run the second CSV file, it tells me "Nothing to be done (a…
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## Bug report
### Expected behavior and actual behavior
When running my pipeline in a normal setting (stubs for making it run quicker) using `nextflow run CenterForMedicalGeneticsGhent/nf-cmgg-…
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https://github.com/raziafrooz/RecountGenotyper/blob/8544ab9bcb2b47d7f75d3003c36e494597bfbcaa/R/GetGenotype.R#L8
If someone wanted to put in a new genotyping model how would they do that? What forma…