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Dear Author,
thanks for the contribution on annotation of SVs, however I have exprericed a difficulty.
when I run the test dataset with following command:
`./svscore.pl -c whole_genome_SNVs.tsv…
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TTAATAATAATAA, T is corresponding to TTAATAATAATAATAATAATAATAATAA ->TTAATAATAATAATAATAATAATAA, TAATAATAATAA.
It seems that it is a problem of extending a haplotype and al…
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Hi,
I have vcf produced by sniffles for SV calling and tried to annotate it with GFF but it produced an empty output.
The below is the bash command I ran.
`vcfanno ./references/chm13.draft_v1…
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Hi,
I have a clean install of bcbio and everything went fine with installation and no errors. While I tried to run sample it gave the following errors
```
[ec2-user@isamples]$ /newvolume/bcbio/…
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An unexpected error has occurred.
Please consider posting the following information to the
conda GitHub issue tracker at:
```
https://github.com/conda/conda/issues
```
Current conda install:
```
…
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**Version info**
bcbio 1.2.8 and 1.2.9.
CentOS Linux release 7.6.1810 (Core)
**To Reproduce**
[](url)
python3 bcbio_nextgen_install.py /mnt/fsx/share/bcbio --tooldir=/mnt/fsx/usr/local --gen…
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Hi!
Q1: Is there a reason that bcbio still uses salmon v1.4.0?
```
[2022-01-21T01:55Z] Version Info: ### PLEASE UPGRADE SALMON ###
[2022-01-21T01:55Z] ### A newer version of salmon with importan…
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I am a student who started my internship at graduate school and is building a new server.
I'm going to install bcbio according to the link recommended by the professor, but I run into the same prob…
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Installing via bcbio results in error "package libtiff-4.3.0-hf544144_1 requires libdeflate >=1.7,
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pcgr 0.10.14
singularity exec ~/beggsa-clinicalnanopore/software/pcgr.sif pcgr --input_vcf /rds/projects/b/beggsa-clinicalnanopore/software/pcgr/test/D0263.vcf.gz --pcgr_dir /rds/projects/b/beggsa-…