FermiKit protocols

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FermiKit specifications

Information


Unique identifier OMICS_09503
Name FermiKit
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Heng Li <>

Publication for FermiKit

FermiKit in pipelines

 (2)
2018
PMCID: 5941068
PMID: 29739910
DOI: 10.1128/mBio.00381-18

[…] criteria to remove false positives: -window 35 -cluster 3 -filtername fs -filter “fs > 30.0” -filtername qd -filter “qd < 2.0.” multisample variant call format (vcf) files were generated using fermikit (). snps were annotated using snpeff (). polymorphic site positions were analyzed using r package adegenet v.2.0.1 ()., we used filtered variants (vcf) to visualize relationships […]

2017
PMCID: 5591230
PMID: 28887485
DOI: 10.1038/s41598-017-10826-9

[…] then mapped back to the reference genome by nucmer. the snv callings from the alignment of assembled contigs were done by the “show-snps” executable in the mummer package. in addition, we applied fermikit to call variants based on de novo assembled unitigs. recall rate and precision were then calculated for three variant calling approaches. finally, variants from the alignment-based […]


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FermiKit in publications

 (3)
PMCID: 5941068
PMID: 29739910
DOI: 10.1128/mBio.00381-18

[…] criteria to remove false positives: -window 35 -cluster 3 -filtername fs -filter “fs > 30.0” -filtername qd -filter “qd < 2.0.” multisample variant call format (vcf) files were generated using fermikit (). snps were annotated using snpeff (). polymorphic site positions were analyzed using r package adegenet v.2.0.1 ()., we used filtered variants (vcf) to visualize relationships […]

PMCID: 5824957
PMID: 29476074
DOI: 10.1038/s41467-018-03244-6

[…] to identify somatic variants, a specific pipeline was developed. for each scc, the union of variants called with haplotypecaller (gatk), mutect2 (gatk 3.5.0), and fermikit version r178 were subjected to further filtering steps. first, the variants present in any of the sccs were gathered in a comprehensive list of interesting positions, which was specific […]

PMCID: 5591230
PMID: 28887485
DOI: 10.1038/s41598-017-10826-9

[…] tool for contig-based variant calling. we observed higher recall rate (0.74 vs. 0.51) but lower precision rate (0.74 vs. 0.94) compared to results from mummer (table ). however, when we used fermikit which would resolve the haplotype of contigs to uncover snvs, its precision and recall rate were very comparable to those yielded from the alignment-based approach (table ). in addition, […]


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FermiKit institution(s)
Broad Institute, Cambridge, MA, USA
FermiKit funding source(s)
NHGRI U54HG003037; NIH GM100233

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