From: Targeted single molecule sequencing methodology for ovarian hyperstimulation syndrome
Primary Analyses | Q metrics | SMRT standard pipeline |
---|---|---|
Secondary Analyses | BLASR de novo CCS aligner algorithm filter v1 (hg19) | BLASR de novo CCS aligner algorithm was used for SNP calling using CCS reads. Reads were filtered by length/quality and mapped to reference sequence (UCSC, hg19). Base quality scores were recalibrated, and consensus Filter v1: Min Read Length bp: 50, Minimum Sub Read Length 50 |
GATK | Overview | Variants identified using the GATK Unified Genotyper for Bayesian diploid and haploid SNP calling using base quality score recalibration and default settings. Indel calling was not included in SMRT pipeline |
ANNOVAR | Functional annotation of variants | |
Data visualization | Overview | SMART view, UCSC Genome browser, R circos plot, Partek |