GeneTalk protocols

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GeneTalk specifications

Information


Unique identifier OMICS_00270
Name GeneTalk
Interface Web user interface
Restrictions to use None
Input format VCF
Computer skills Basic
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/GeneTalk

Taxon


  • Primates
    • Homo sapiens

Publication for GeneTalk

GeneTalk in pipeline

2016
PMCID: 5084765
PMID: 27120253
DOI: 10.1002/humu.23006

[…] primer pair sequences and qpcr settings are available upon request. all sequence variants described in the manuscript have also been submitted to clinvar (http://www.ncbi.nlm.nih.gov/clinvar/) and genetalk (http://gene‐talk.de/targetlections/35134)., short‐read fragments from high‐throughput sequencing were first mapped to the human reference genome grch37 with bwa‐mem, and cdna alignments […]


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GeneTalk in publications

 (11)
PMCID: 5565107
PMID: 28827829
DOI: 10.1371/journal.pone.0183438

[…] interest was eluted and subjected to 18 cycles of dna amplification. the sample was then sequenced using an illumina hiseq2000 sequencer (illumina, san diego, ca, usa). the data were filtered using genetalk (http://www.gene-talk.de) []. variants were analyzed with polyphen-2 (http://genetics.bwh.harvard.edu/pph2/) and sift (sorting intolerant from tolerant web server, version 5.1.1, database […]

PMCID: 5343999
PMID: 28241424
DOI: 10.3390/ijms18020467

[…] loci led to repeat mapping of the reads to a synthetic caucasian major allele reference sequence (ceu-mars) [], following the same process illustrated in . resulting vcfs were then processed using genetalk [], a web-based tool for filtering and annotation of uploadable vcfs., a coverage depth of 15× was used for detection of potentially causative gene variants, prior to confirmation by sanger […]

PMCID: 5408770
PMID: 27565584
DOI: 10.1093/bioinformatics/btw550

[…] as well as increasing degrees of error rates we also simulated samples based on sequencing data from real individuals. the java application, as well as the visualizing r script, is integrated in genetalk (), and also available as a standalone application at www.gene-talk.de/vcf2ped. we analyzed the performance of our approach for a decreasing number of exomic and genomic markers. for exomic […]

PMCID: 4935805
PMID: 27380894
DOI: 10.1038/ncomms11920

[…] removed duplicated reads were further technically analysed using the seqmonk program version v0.25.0 (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk). variant filtering was performed by genetalk (https://www.gene-talk.de/)., mutation screening of mbtps2 and segregation analysis of the mutation within the family was performed by fluorescent bidirectional sequencing of genomic […]

PMCID: 4678573
PMID: 26666243
DOI: 10.1186/s40246-015-0055-x

[…] settings optimized for germ-line high frequency variants and minimal false positive calls. the output variant call format (vcf) file was then annotated through the web-based user-interfaced genetalk (genetalk gmbh, berlin, germany) and ensembl variant effect predictor []., sequence variants were compared with data in dbsnp, 1000 genomes and human genome mutation database. variants […]


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GeneTalk institution(s)
GeneTalk, Berlin, Germany; Department of Medical and Human Genetics, Charité, Univfersitätsmedizin Berlin,Berlin, Germany

GeneTalk review

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Anonymous user #122

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Web
GeneTalk is a perfect platform to analyze VCF files and to get into contact with experts: We needed a to be able to contact any geneticist in the world that’s an expert for a specific gene. Now we can make use of social web technology at GeneTalk to find second patients with a particular variant or colleagues to collaborate with.