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Table 1 Data pipeline

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