cpipe

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Numerous scripts along the pipeline expects .bed.cov files format to be something along ``` chr1 start end name offset coverage ``` When their actual format is ``` chr1 start end...

marnec

Pipeline fails since variant_effect_predictor.pl is no more there in version 95

marnec

links to VEP files and Human reference are outdated

marnec

Less, I'm thinking, a problem with cpipe and more, most likely, I'm missing something basic. I have a pre-existing install of VEP, on a server that loads everything as modules...

tirohia

I want to test other BED file for the same batch. Is there a way to rerun a batch from the point it starts using a BED file? Maybe to...

biocyberman

multimeric

What replaced annovar?

2

https://github.com/MelbourneGenomics/cpipe/blob/dev/docs/outputs.md This document says annovar is deprecated. That caught me by surprise because annovar is still frequently found in many places in Cpipe's existence: publication, features, user guide, roadmap, etc....

biocyberman

Hi I am testing out cpipe 2.5.1 vcfanno is configured to use this annotation source. However, the installation process does not allow downloading data for vcfanno. Can I use this...

biocyberman

Cpipe checks that the input file's extensions are a subset of {fastq, gz}, when it should just check that it ends in `.fastq.gz`: https://github.com/MelbourneGenomics/cpipe/blob/642afa87495746dc7412ba1dd3b8b9a775f2ddf2/lib/cpipe/metadata_schema.py#L32

multimeric

numerous problems with installation

3

I am running installation with tag v2.5.1 from dev branch. There are many problems which can cause the installation to quit. I am fixing some of them, will I submit...

biocyberman