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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

 (6)
call_split

The impact of genotype calling errors on family based studies

2016
Sci Rep
PMCID: 4916415
PMID: 27328765
DOI: 10.1038/srep28323
call_split See protocol

[…] amilial correlations into account, it leads to lower accuracy of calls, especially for low depth sites (e.g. 6X). Therefore, we applied two existing family-based genotype-calling methods, Beagle4 and Polymutt, to re-call the genotypes at sites with depth of 6X. […]

library_books

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

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

[…] Initial 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 into distinct […]

library_books

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

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

[…] re 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

FamSeq: A Variant Calling Program for Family Based Sequencing Data Using Graphics Processing Units

2014
PLoS Comput Biol
PMCID: 4214554
PMID: 25357123
DOI: 10.1371/journal.pcbi.1003880

[…] software packages have been implemented to incorporate pedigree information for variant calling. SAMtools and DeNovoGear can process family trios together. The Elston-Stewart algorithm was used in PolyMutt to incorporate extended families. However, the Elston-Stewart algorithm requires either loop-cutting techniques, which will substantially increase the computing time and give approximate ans […]

library_books

Using familial information for variant filtering in high throughput sequencing studies

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

[…] mily-oriented 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 a […]

library_books

Variant Callers for Next Generation Sequencing Data: A Comparison Study

2013
PLoS One
PMCID: 3785481
PMID: 24086590
DOI: 10.1371/journal.pone.0075619

[…] ols [], GATK [,], and Atlas2 []. presents simple summaries of their characteristics. SAMtools uses a revised MAQ model to estimate sequencing error. The glftools family (glfSingle, glfMultiples, and polymutt) call SNPs from pre-generated genotype likelihood files (GLF). GATK adopts the MapReduce philosophy [] to parallel programming for simple Bayesian modeling. Atlas2 employs logistic regression […]

Citations

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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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