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Good morning,
I am testing your sarek pipeline and I am experiencing some problems with the annotation step. Until now, I am just using the test dataset.
After the whole pipeline failed to annot…
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Greetings,
We are excited to check out SnpEff v5.0.0 but it appears that some of the databases we are interested in are not able to be downloaded right now.
If we look at the output of the "data…
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**Version info**
Version: 1.2.7 (or latest version per bcbio_nextgen_install.py)
OS name:/version: CentOS Linux release 7.8.2003 (Core)
OS environment: HPC cluster
**To Reproduce**
wget command…
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tested on usegalaxy.eu (19_05) and SnpEff build
We can use `Simple inputs used for workflow logic` as input parameter for `Remove sequence version label` as it's a Boolean.
We can't use `Simple …
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The current pipeline output shows outputs from zipped HTML that are unreadable and JSON that has little visual value.
The [IRIDA code](https://github.com/apetkau/irida/blob/development/src/main/jav…
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I have a huge list of CSQ fields and I tried to extract all of them from VEP annotated VCF into tab seperated fields using
`bcftools +split-vep -f '%CHROM\t%POS\t%REF\t%ALT\t%CSQ\n' -d -A tab inpu…
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Hi there - I have downloaded dbNSFPv4.1a from the website and am trying to create a database for snpSift to use. I followed the instructions on this page.
https://pcingola.github.io/SnpEff/ss_dbnsfp…
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Hi Cyriac,
I am trying to run vcf2maf for my exome data. Here is the error I keep getting?
Use of uninitialized value in pattern match (m//) at vcf2maf.pl line 787, line 109.
Use of uninitialized va…
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Hi all,
I am kinda new to this field, so my apologies in advance.
I am trying to run SnpEff on my Mac using Anaconda. I think I managed to install the package (conda install -c bioconda snpeff)…
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- how many genes have snps
- % nonsynonmyoys , synonymous
- transition a t g c