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Protocols

Polymutt specifications

Information


Unique identifier OMICS_00088
Name Polymutt
Alternative names Polymorphism and Mutation discovery, Polymutt2
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format GLF
Output data Variant calls
Output format VCF
Operating system Unix/Linux
Computer skills Advanced
Version 0.18
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Bingshan Li <>

Additional information


http://www.pitt.edu/~wec47/polymutt.html

Publication for Polymorphism and Mutation discovery

Polymutt citations

 (4)
library_books

The impact of genotype calling errors on family based studies

2016
PMCID: 4916415
PMID: 27328765
DOI: 10.1038/srep28323

[…] that low read-depth leads to a greater reduction in the proportion of transmitted alleles (), and thus a more inflated type i error rate at the gene level (). indicates that the beagle4 and polymutt re-called genotypes result in reduced inflation in terms of type i error rate, but the false positive effect is still considerable. furthermore, larger genes are more likely to be affected […]

library_books

Sequencing strategies and characterization of 721 vervet monkey genomes for future genetic analyses of medically relevant traits

2015
PMCID: 4494155
PMID: 26092298
DOI: 10.1186/s12915-015-0152-2

[…] variant calling of the alignment files used samtools []. due to the size and complexity of the vrc pedigree, we were unable to refine these genotype calls using pedigree-aware methods such as polymutt []. we therefore broke the pedigree into units (trios and parent-offspring duos) that could be analyzed with the programs triocaller [] and beagle 4.0 []. we broke full sibships […]

library_books

Exome sequencing of case unaffected parents trios reveals recessive and de novo genetic variants in sporadic ALS

2015
PMCID: 4360641
PMID: 25773295
DOI: 10.1038/srep09124

[…] is inherently biased towards the creation of false positives. for this reason we imposed several quality control steps in an attempt to filter out false positives. for the de novo variants we used polymutt software that takes into account the parental genotypes when calling a de novo variant in the offspring. of the variants that did not validate, 14 were due to poor sanger data quality in one […]

library_books

Using familial information for variant filtering in high throughput sequencing studies

2014
PMCID: 4185103
PMID: 25129038
DOI: 10.1007/s00439-014-1479-4

[…] hts analysis pipeline can also produce mendelian consistent genotype data from hts data by making use of variant callers that incorporate familial information. famseq (peng et al. ) and polymutt (li et al. ) improve variant calling by making use of familial information while mate-clever (marschall et al. ) performs family aware indel detection and calling. once hapmap snp genotypes […]


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Polymutt institution(s)
Center for Human Genetics Research, Department of Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA; Department of Pediatrics, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA; Center for Statistical Genetics, Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA; Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Italy

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