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Dear Aldy Team,
I analyzed targeted sequencing data of 100 PGx genes aligned to the hg19 reference genome using both BAM and VCF files in Aldy v4.4 (Python 3.9.7 on Linux 3.10.0-1160.95.1.el7.x86_6…
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### Oxford Nanopore
- [NA12878](https://github.com/nanopore-wgs-consortium/NA12878) WGS data
### PacBio
- PGV001 patients
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- [ ] Look at the [list](https://docs.google.com/spreadsheets/d/1wNtmceBQwZu71gmQ1Z48yqNdV0zNu9WfZJ5IAhoRnMw/edit#gid=845169585) of data types cohorts are collecting and determine existing nextflow/CW…
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>>
>> https://github.com/rmcolq/pandora/blob/815da22867f2bdaa3e3bf40f382be830c1506b0a/src/estimate_parameters.cpp#L217-L231
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>> In particular https://github.com/rmcolq/pandora/blob/815da22867f2…
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STAR-Fusion was developed for illumina data,
we have tried running it on ultima genomics data, which is 300bp single-end reads. STAR-Fusion works. But with Ultima, there are no 'SpanningFrag' / dis…
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For example,
Simply changing
**a**cerates viridiflora (raf.) eaton
https://api.gbif.org/v1/species/match?name=acerates%20viridiflora%20(raf.)%20eaton
to
**A**cerates viridiflora (raf.) eaton…
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Hi，when I run IsoCon，I found the results vary greatly with different --min_candidate_support set. So I wonder how to set this parameter is ok？
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Hello,
I get empty files HPVfusionPointContig and ContigSequence.fa.
Also, you left your paths to the tools in the scripts and some of the tools you are using are very old versions (GATK, Pear).…
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## Description of the bug
Running Sarek with `-r dev` and using a capture / targeted BED runs into trouble with ControlFreec.
https://github.com/BoevaLab/FREEC/issues/106 for more context, @Fri…
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Hi,
Can you please give a suggestion on how to use SEACR with experiments that have spike-in and replicates. What do you recommend as far as normalization with spike-in and how to handle replicates?
…