vcflib protocols

vcflib specifications

Information


Unique identifier OMICS_02112
Name vcflib
Alternative name libvcflib
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format VCF
Output format VCF
Operating system Unix/Linux
Programming languages C++
License MIT License
Computer skills Advanced
Stability Stable
Maintained Yes

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vcflib IN pipelines

 (9)
2018
PMCID: 5887293
PMID: 29617811
DOI: 10.1093/gbe/evy061

[…] t al. 2012)., the b. rapa snps were called from the transcriptomes of 126 accessions (qi et al. 2017), and also annotated with snpeff. low quality snps were removed with vcffilter (https://github.com/vcflib/vcflib; last accessed march 21, 2018) and vcftools (danecek et al. 2011): only snps identified in regions with read depth >10 and root mean square mapping quality >30 were used for subseq […]

2018
PMCID: 5887293
PMID: 29617811
DOI: 10.1093/gbe/evy061

[…] the b. rapa snps were called from the transcriptomes of 126 accessions (qi et al. 2017), and also annotated with snpeff. low quality snps were removed with vcffilter (https://github.com/vcflib/vcflib; last accessed march 21, 2018) and vcftools (danecek et al. 2011): only snps identified in regions with read depth >10 and root mean square mapping quality >30 were used for subsequent […]

2018
PMCID: 5940669
PMID: 29740198
DOI: 10.1038/s41598-018-25669-1

[…] sensitivity (i.e. minimum variant frequency for indels was set to 0.05 instead of 0.15; complex variant detection was enabled). called variants were annotated using a custom pipeline based on vcflib (https://github.com/ekg/vcflib), snpsift37, the variant effect predictor (vep) software38 and ncbi refseq database. confident somatic mutations were obtained from annotated variants by: i) […]

2018
PMCID: 5940669
PMID: 29740198
DOI: 10.1038/s41598-018-25669-1

[…] variant frequency for indels was set to 0.05 instead of 0.15; complex variant detection was enabled). called variants were annotated using a custom pipeline based on vcflib (https://github.com/ekg/vcflib), snpsift37, the variant effect predictor (vep) software38 and ncbi refseq database. confident somatic mutations were obtained from annotated variants by: i) filtering-out germline mutations […]

2017
PMCID: 5389967
PMID: 28450881
DOI: 10.3389/fgene.2017.00044

[…] using vcftools (danecek et al., 2011) and the r package popgenome (pfeifer et al., 2014). an element was considered as complete if its size was at least 90% of the maximum size for its family. the vcflib script vcffilter6 was used to split vcfs between complete and truncated elements for each family., to assess whether line variation deviated from a neutral model, we estimated the demographic […]

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