NGS SNP & Indel Expertise

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Overview of NBIC genomic variant calling activities

Variant calling modules and NBIC users

A nice CNV visualization tool developed by our member group at Hubrecht:

Category Package Description Performance experience NBIC user Latest update
Indel Pindel pubmed None Ka Ye in LUMC
SNP/indel VarScan VarScan, an open source tool for variant detection that is compatible with several short read align-ers. pubmed None Matt
SNP/indel VARid A Hidden Markov Model for representing both color-space and letter-space reads together, and a framework for determining variation without diret translation of those reads (ISMB 2009). None
SNP/Indel Discovery SOAPsnp SOAPsnp is an accurate consensus sequence builder based on soap1 and SOAPaligner/soap2\'s alignment output. It calculates a quality score for each consensus base, which can be used for any latter process to call SNPs. None Victor
SNP/Indel Discovery ssahaSNP ssahaSNP is a polymorphism detection tool. It detects homozygous SNPs and indels by aligning shotgun reads to the finished genome sequence. Highly repetitive elements are filtered out by ignoring those kmer words with high occurrence numbers. More tuned for ABI Sanger reads. Developers are Adam Spargo and Zemin Ning from the Sanger Centre. Compaq Alpha, Linux-64, Linux-32, Solaris and Mac None
SNP/Indel Discovery PolyBayesShort A re-incarnation of the PolyBayes SNP discovery tool developed by Gabor Marth at Washington University. This version is specifically optimized for the analysis of large numbers (millions) of high-throughput next-generation sequencer reads, aligned to whole chromosomes of model organism or mammalian genomes. Developers at Boston College. Linux-64 and Linux-32. None
SNP/Indel Discovery PyroBayes PyroBayes is a novel base caller for pyrosequences from the 454 Life Sciences sequencing machines. It was designed to assign more accurate base quality estimates to the 454 pyrosequences. Developers at Boston College. None
SNP/Indel Discovery ROAST ROAST is a stand-alone tool that can handle both short read and pyrosequencing data (454, Roche) to determine SNP/InDels. We introduce a number of novel criteria that provide more complete information to judge whether a putative SNP/InDel is actually present or not where current algorithms merely produce a list of SNPs/InDels for a given sequence. ROAST runs on any linux distribution with a minimum of requirements and very rapidly provides the user with a short-list of SNPs/InDels identified in a short-sequence or pyrosequencing data set compared to a reference sequence. Output options are variant lists / Annotated GenBank and CDS changes based on the variants detected (synonymous/non-synonymous SNP's for example). Compared to existing tools, SNP/InDel detection by ROAST is very sensitive and specific. Performance is slightly less than MAQ or Soapsnp but the output is much more accessible for biologists and annotators. Victor, Sacha van Hijum and collaborators Dec. 2009
SNP/Indel Discovery SAMTools SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. Both Bowtie and BWA can generate output into SAM and BAM format and link nicely with SAM tools. Galaxy has a built-in SAM toolbox. Frans Paul, Jeroen Laros.