vcf2maf
snippy
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vcf2maf | snippy | |
---|---|---|
2 | 6 | |
355 | 437 | |
2.3% | - | |
0.0 | 3.9 | |
4 months ago | 6 months ago | |
Perl | Perl | |
GNU General Public License v3.0 or later | GNU General Public License v3.0 only |
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vcf2maf
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Convert VCF to MAF in Bioconductor?
This is not a part of Bioconductor, but I used this one here: https://github.com/mskcc/vcf2maf
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What is the difference between information in maf files and vcf?
There is a perl script called vcftomaf from here https://github.com/mskcc/vcf2maf
snippy
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Help/recommendations for whole genome sequence analysis
This should be of help, if you think you can get have a decent (closely related) reference genome from NCBI: https://github.com/tseemann/snippy
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Software to automatically detect SNP's between 2 or more genomes?
snippy is a nice tool for this!
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Microbiome - would it be reasonable to assume that a bacterial contaminant (eg during library prep) would be the same isolate across contaminated samples?
So, let's say I have a batch of 20 samples, and I found evidence for my genus of interest in 5. What I've done is used Snippy (https://github.com/tseemann/snippy) with mapping based on a reference species in the genus. Snippy finds shared "core" regions of the reference species that are present in all samples and compares the SNPs between the samples. I find that each sample has distinct SNPs, which I believe indicates that the bacteria in each sample are not the same isolate. Thus, I am trying to argue that the bacteria could not have come from a shared contamination event during library prep. Does this make things more clear?
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How to find sequence variations from contigs
My first idea was to assemble the contigs into scaffolds (e. g. using RagTag) and then look for a tool that can identify these mutations. However, I've also come across snippy, which is a tool that can identify mutations from reads. I don't know if I can just apply it to contigs though (probably not).
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Sorting reads to references with high identity
I would use snippy for this if there references are haploid genomes https://github.com/tseemann/snippy
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Inquiry regarding Snippy (by Seemann). My job has been running for more than 5 days with no update. Can anyone help me?
[18:37:12] Obtained from https://github.com/tseemann/snippy
What are some alternatives?
postgresqltuner - Simple script to analyse your PostgreSQL database configuration, and give tuning advice
dipcall - Reference-based variant calling pipeline for a pair of phased haplotype assemblies
Rsnapshot - a tool for backing up your data using rsync (if you want to get help, use https://lists.sourceforge.net/lists/listinfo/rsnapshot-discuss)
tronflow-vcf-postprocessing - A Nextflow variant normalization pipeline based on vt and bcftools
mojo - The Mojo Programming Language
RagTag - Tools for fast and flexible genome assembly scaffolding and improvement
ImapSync - Imapsync is an IMAP transfers tool. The purpose of imapsync is to migrate IMAP accounts or to backup IMAP accounts. IMAP is one of the three current standard protocols to access mailboxes, the two others are POP3 and HTTP with webmails, webmails are often tied to an IMAP server. Upstream website is
exiftool - ExifTool meta information reader/writer