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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
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