Stampy protocols

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Stampy computational protocol

Stampy specifications

Information


Unique identifier OMICS_00691
Name Stampy
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data FASTQ,FASTA,GZIPPED,SAM,BAM
Output data SAM
Biological technology Illumina
Operating system Unix/Linux, Mac OS
Programming languages Python
Computer skills Advanced
Version 1.0.20
Stability Stable
Registration required Yes
Maintained Yes

Versioning


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Maintainer


  • person_outline Gerton Lunter <>

Additional information


http://www.well.ox.ac.uk/~gerton/README.txt

Publication for Stampy

Stampy IN pipelines

 (19)
2017
PMCID: 5408089
PMID: 28402527
DOI: 10.1093/gbe/evx068

[…] for paired- and single-end reads, we randomly selected one read per pair from paired-end data from the original 99 individuals to use for further analysis., all sequence data were mapped using stampy 1.0.21 (lunter and goodson 2011) with default settings to an exon-only reference generated from the capsella rubella reference genome (josephs et al. 2015; slotte et al. 2013). capsella […]

2016
PMCID: 4777131
PMID: 26772750
DOI: 10.1534/g3.115.023655

[…] of these samples (all samples had percentage of mapped reads within 1% of the percentage of mapped reads for the resequenced run)., reads for parents and offspring were aligned to hmel1.1 using stampy (lunter and goodson 2011) version 1.0.23 with options -substitution-rate = 0.01 and —gatkcigarworkaround and converted from sam to bam format with the sortsam tool from picard version 1.117 […]

2016
PMCID: 4848515
PMID: 27108815
DOI: 10.1038/ncomms11414

[…] cdnas from cells of interest were then subjected to illumina sequence library preparation and sequencing on an illumina hiseq 2500., sequence reads were mapped to the mm9 mouse genome release with stampy using default parameters55. read pairs with identical outer coordinates were reduced to a single pair. numbers of remaining properly paired reads per sample are reported in supplementary table […]

2016
PMCID: 4906373
PMID: 27239039
DOI: 10.1016/j.celrep.2016.04.090

[…] using standard procedures, captured using the sureselect human all exon kit (agilent technologies), and then sequenced using illumina technology. the 51-bp paired-end reads were mapped using stampy (lunter and goodson, 2011), and duplicate pcr reads were removed using picard (http://picard.sourceforge.net/). single-nucleotide variants were called using platypus (rimmer et al., 2014)., […]

2016
PMCID: 4915495
PMID: 26818911
DOI: 10.1002/jbmr.2797

[…] of the coding exome, as specified by the consensus coding sequence (ccds) project,16 in both individuals. reads were aligned to the human sequence version 37d5 (hs37d5) reference genome using stampy17 and variant calling of single nucleotide variants (snvs) and short insertions and deletions (indels) was undertaken using platypus (v0.5.1).18 analysis of coding variants was undertaken […]

Stampy institution(s)
Wellcome Trust Centre for Human Genetics, Oxford, UK
Stampy funding source(s)
Supported by the Wellcome Trust, grant no. 075491/Z/04.

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