pone.0296785.s002.xlsx (6.23 kB)
Complete validation results.
dataset
posted on 2024-01-18, 18:35 authored by Dhanaprakash Jambulingam, Venkat Subramaniam Rathinakannan, Samuel Heron, Johanna Schleutker, Vidal FeyIn the revision process, the pipeline was validated on gold standard data sets HG003, HG004, HG006 and HG007, data sets generated with the same sequencing protocol in the same study as data sets HG001, HG002 and HG005. The table shows the number of variants identified by each variant caller, their precision and recall values. *The table contains only SNP information.
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throughput sequencing technologiesstandard sequencing methodspipeline scripting languagekuura &# 8212quality score recalibrationconsensus call filegatk haplotypecaller wgs data ”,div >< p2 ), generatingvariant calling stepvariant recalibrationvariant consensusvariant callingvarscan strelka nextflow freebayes docker deepvariant whole exomeupdating toolstime associatedsource coderesearch gapresearch communityreference genomepublicly availableoptimal resourcesimportant featuregithub repositorygenomic sciencesfragmented toolseasily extendeddifferent projectscopious amountconfidence variantsavailable toolsalso presented
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