SolSNP

[…] AST [] was used for all alignments. Indels and reads mapping to multiple locations were removed from the final alignments. Each alignment was analyzed for single nucleotide polymorphisms (SNPs) using SolSNP (http://sourceforge.net/projects/solsnp/). Only loci that had a minimum coverage of 10X and the base variant was present in greater than 90% of the calls, were included in the final analysis. A […]

[…] BWA-MEM [] or NUCmer [], respectively. SNPs and insertion/deletions (indels) can be identified with variant callers including the UnifiedGenotyper method in GATK [, ], SAMtools [], VarScan [], and/or SOLSNP ([]). Called SNPs can then filtered using user-defined thresholds for read depth (default = 3×) and allele frequency proportion (default = 90 %). All called SNPs are then placed into a matrix t […]

[…] es from 2004 to seven genomes from the Bahrain outbreak. Using ATCC 23344 genome as a reference, we identified homologous regions using MUMmer , and found single nucleotide polymorphisms (SNPs) using SolSNP ((http://sourceforge.net/projects/solsnp/). After eliminating potential paralogs and positions with missing or ambiguous data among isolates, raw reads containing SNPs were aligned to the refer […]

[…] amples. A number of somatic mutation tools have emerged in the past 2 years, including deepSNV, Strelka, MutationSeq, MutTect, QuadGT (http://www.iro.umontreal.ca/~csuros/quadgt), Seurat, Shimmer and SolSNP (http://source-forge.net/projects/solsnp), jointSNVMix, SomaticSniper, VarScan2, and Virmid. Each of them is equipped with unique features and applications. For example, deepSNV was specially d […]

[…] the 11819-97 reference genome using the short-read alignment component of the Burrows-Wheeler aligner (), and external genomes were aligned using MUMmer (). Each alignment was analyzed for SNPs using SolSNP (http://sourceforge.net/projects/solsnp/) and excluded all SNPs that did not meet a minimum coverage of 10 or if the variant was present in <90% of the base calls for that position. SNPs identi […]

[…] To identify putative SNPs, homologous genomic regions were identified using MUMmer and aligned to search for SNPs using SolSNP (http://sourceforge.net/projects/solsnp/). We ensured site orthology by eliminating potential paralogs and requiring all genome alignments to include 100 bp flanking each side of the SNP. Furth […]