Improving SNP discovery by base alignment quality

By Heng Li. Bioinform., 2011

306 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/047e556702b291acc1c19ada548b746f14fe879f

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Citations in the corpus

Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly (2012, methodology): “wski et al., 2008; Krawitz et a l., ∗to whom correspondence should be addressed 2010), iterative mapping (Manske and Kwiatkowski, 2009), read realignment (Albers et al., 2010; Homer and Nelson, 2010; Li, 2011; Depristo et al., 2011) and local assembly (Carnevali et al., 2011). However, because these”
A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data (2011, methodology): “e ‘2log’ scale as in D p, SomaticSniper identiﬁed 1,826 differences. SAMtools called fewer because it limits the mapping quality of reads with excessive mismatches and applies base alignment quality (Li, 2011) to ﬁx alignment errors around INDELs. With the two features switched off, SAMtools called ”
Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing (2017, methodology): “For each library, we sampled 100 000 reads from the reads mapped to the reference genome using samtools (v. 1.2; SAM-TOOLS, RRID:SCR 002105) [94, 95] and seqtk (v. 1.0) [96].”
Toward better understanding of artifacts in variant calling from high-coverage samples (2014, methodology): “Platypus and SAMtools may produce many overlapping variants.”
Using Drosophila melanogaster as a Model for Genotoxic Chemical Mutational Studies with a New Program, SnpSift (2012, methodology): “When using individual calls without base alignment quality (BAQ) model, (Li, 2011) a total of 1,036,435 homozygous SNPs were detected.”
ANGSD: Analysis of Next Generation Sequencing Data (2014, methodology): “01-snp_pval 2) using local qscore recalibration with the BAQ model [35] -baq 3) SAMtools or GATK GL model -GL.”
Twelve years of SAMtools and BCFtools (2020, background): “The calculation takes into account mapping qualities of the reads, base qualities and the probability of local misalignment, per-base alignment quality (BAQ)[9].”