snptools  (RStudio)

Journal: Genome Research

Article Title: An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data

doi: 10.1101/gr.146084.112

Figure Lengend Snippet: Overview of the SNPTools Pipeline. The SNPTools pipeline utilizes binary sequence map (BAM) files and then processes them through four modular steps: calculation of effective base depth (EBD), SNP site discovery, BAM-specific binomial mixture modeling (BBMM) to calculate genotype likelihoods, and genotype and haplotype imputation.

Article Snippet: SNPTools can be found at http://sourceforge.net/projects/snptools/ .

Techniques: Sequencing

Journal: Genome Research

Article Title: An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data

doi: 10.1101/gr.146084.112

Figure Lengend Snippet: SNP statistics for sites discovered in 1000G PHASE1 with SNPTools. SNP sites were discovered using the variance ratio statistic. The unfiltered autosomal site list was composed of 34,656,295 candidate SNP sites, with an average Ti/Tv ratio of 2.11. SNPs were filtered using four criteria (Supplemental Material) to produce a final list of 32,737,954 SNPs with a Ti/Tv ratio of 2.15. ( A ) We found that 78.3% of the ∼32.7 million SNP were novel when evaluated with dbSNP 129. These novel sites had a Ti/Tv ratio of 2.15, which was comparable to the Ti/Tv of known sites, 2.17. ( B ) The site frequency spectrum of our discovered SNPs reveals that most novel SNPs were rare with MAF < 0.5%. ( C ) We provide discovery statistics for Chr20 and for the whole genome. Known SNPs are defined as being present in dbSNP129. SNPTools had a low false-discovery rate of 1284 sites out of 99,817 monomorphic OMNI sites.

Article Snippet: SNPTools can be found at http://sourceforge.net/projects/snptools/ .

Techniques:

Journal: Genome Research

Article Title: An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data

doi: 10.1101/gr.146084.112

Figure Lengend Snippet: Genotype discordance rates for SNPTools and Beagle

Article Snippet: SNPTools can be found at http://sourceforge.net/projects/snptools/ .

Techniques:

Journal: Genome Research

Article Title: An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data

doi: 10.1101/gr.146084.112

Figure Lengend Snippet: Haplotype phasing accuracy evaluation. SNPTools and Beagle are compared against the benchmark haplotypes from the 1000G Phase 1. ( A ) Switch accuracy between SNPTools and Beagle showed that SNPTools had higher switch accuracy. ( B ) While SNPTools had moderately worse performance on incorrect genotype percentage (IGP) for admixture populations (American [AMR] and African [AFR]), it showed comparable performance on all other populations. ( C ) Incorrect haplotype percentage (HIP) for AFR samples (representative of all populations). Phasing by SNPTools and Beagle were comparable until 100 kb [log 10 (100kb) = 2]. At longer distances, SNPTools was moderately more accurate than Beagle. ( D ) Phasing by SNPTools on AFR, Asian (ASN), AMR, and European (EUR) populations shows that AFR samples were more likely to be incorrectly phased at a given distance (data not shown). However, at 100 kb, all populations have an HIP of 65%–70%.

Article Snippet: SNPTools can be found at http://sourceforge.net/projects/snptools/ .

Techniques: