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Hello,
While trying to run PTATO 1.3.3 I had an issue with pulling the SnpSift container:
https://github.com/ToolsVanBox/PTATO/blob/eafc29c4d887b4ba4795cb9cbff401e9bc621ef5/NextflowModules/SnpSi…
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Hi,
I'm trying to use `gtfilter` (or `Filter GT`) module to set individual genotype calls to missing (`"."`) if they match a certain criteria.
I managed to do so when filtering based on a minimum de…
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Bonjour
Cette commande semble enlever ('filter out') le contenu du fichier SRR13182925.ann.vcf.
SnpSift filter "(exists ANN[0].HGVS_P)" > SRR13182925.ann.vcf
Elle se trouve dans ce fichier: blog/co…
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The tool failed with error missing Java
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Hi @bentsherman
Thank you so much for sharing `ǹf-boost`, the `cleanup` fonctionality is eagerly awaited by many users, including us :)
I made a first test case, and I would like to share my res…
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#### Description
Empty outputs are generated in tumor-only analysis when including numbered GEN[1] fields with a higher number than 0. This issue needs to be investigated and resolved to ensure cor…
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Hi,
I have a 3.8Gb VCF file produced by a WGS pipeline mapping on hg38 and mutation calling using Mutect2.
The file contains chromosomes chr1 ... chr22, chrX, chrY and chrM in that order.
Run…
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# Poretools
- [ ] Add link to [readthedocs](https://poretools.readthedocs.io/en/latest/content/examples.html)
# SNPEff
- [ ] It is absolutely unclear how to use `SNPEff download` and `SNPEf…
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I'm not familiar with snpeff and filter snv
i try
```
java -jar snpEff.jar databases|grep gnomad
```
i can't found anything
mabey i should[ build database](http://pcingola.github.io/SnpEff/s…
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Thank you for SnpSift, what a powerful useful program! I'm new to SnpSift, and have a basic question - the VCF file I'm starting with already has an INFO.AF field. I want to annotate the VCF file with…