Detailed description of CoVaCS pipelines.doc

DetaileddescriptionofCoVaCSpipelinesQualitypreprocessingandoutlineAfterpreprocessingofdatausingTrimmomatic[1]program()readsarealignedtogenomicindexesretrievedfromtheIlluminai-genomesrepository(http://support./sequencing/sequencing_software/)withBowtie2[2].PCRduplicatesareremovedusingtheMarkDuplicatesutilityfromthePicard[3]toolsuite()pressionofalignmentfilesisperformedwithSamtools[4]-(jsp)andsingle-sample(ssp),[5,],,isappropriateforindividualandsmall-,sspproceduresshowsimilarsensitivityandspecificitytojoint-samplecallingstrategies,althoughperformancecanbeimpairedwhentheseconditionsarenotsatisfied[6].STEPA:QualitytrimmingSincevariantcallingalgorithmsaremorerobusttosequencingerrorsthantoreducedcoverage,relativelyrelaxedsequentialpre-processingstepsareperformedusingTrimmomatic[1]).AnyadaptersequencesinthesequencedataareremovedThe“Leading”flagremovesnucleotidesfromthe5'endofthereadsiftheirqualityscorefallsbelowapredefinedcutoff(Q<=5)“Trailing”whichperformstheequivalentoperationonthe3'endofreads“Slidingwindows”evaluatestheaveragequalityscoresofthereadsalongslidingwindowsoffixedlength(4bp),cuttingthereadoncetheaveragequalitywithinthewindowfallsbelowathreshold(Q<=15)Readsshorterthan50bpsaftertrimmingdiscardedandthefastQCprogramusedtogeneratediagnosticreportsontrimmedanduntrimmedreadstofacilitateevaluationoftheefficacyofpre-:AlignmentandAlignmentpostprocessing Readsarealignedtothereferencegenom