SNPSVM statistics

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Associated diseases

Associated diseases

SNPSVM specifications

Information


Unique identifier OMICS_03838
Name SNPSVM
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data An alignment of sequencing reads.
Input format BAM,SAM
Output data A file describing where all the SNPs (single nucleotide polymorphisms) are.
Output format VCF
Operating system Unix/Linux
Programming languages Java, Python
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Maintainers


  • person_outline Brendan O'Fallon <>
  • person_outline David Crockett <>

Publication for SNPSVM

SNPSVM in publication

PMCID: 4619817
PMID: 26539496
DOI: 10.1155/2015/456479

[…] aligners (bowtie2 [], bwa sampe [], bwa mem [], cushaw3 [], mosaik [], and novoalign) and five variant callers (freebayes [], gatk haplotypecaller, gatk unifiedgenotyper [], samtools mpileup [], and snpsvm []). in this study we also try to determine how much of an effect, if any, the aligner has on variant calling and which aligners perform best when using a normal illumina exome sample. […]


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SNPSVM institution(s)
ARUP Institute of Clinical and Experimental Pathology, Salt Lake City, UT, USA
SNPSVM funding source(s)
Supported by ARUP Institute for Clinical and Experimental Pathology.

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