BLUPf90&PreGSandQualityControl

PreGSf90

•  Interfaceprogramtothegenomicmoduletoprocessthegenomicinforma@onfortheBLUPF90familyofprograms

•  Efficientmethods–  crea@onofthegenomicrela@onshipmatrix,rela@onshipbasedonpedigree

–  Inverseofrela@onshipmatrices

•  PerformsQualityControlofSNPinforma@on

BLUPF90programsusingGenomic

•  Genomicprograms– controledbyaddingOPTIONScommandstotheparameterfile

– OPTION SNP_file marker.geno.clean

– Read2files:•  marker.geno.clean •  marker.geno.clean_XrefID

OutputFiles•  GimA22i

–  Storethecontentoftheinv(G)–inv(A22)–  OnlyifpreGSf90forruns,notinapplica@onsprograms

•  freqdata.count–  Containsthees@matedallelefrequencybeforeQC

•  freqdata.count.aUer.clean–  Containsallelefrequenciesasusedincalcula@ons,removecode–  ForremovedSNPthesewillbezero

•  Gen_call_rate–  Listofanimalsremovedbylowcallrate

•  Gen_conflicts–  ReportofanimalswithMendelianconflicts

QualitycontrolBydefaultexclude

•  MAF– SNPwithMAF<0.05

•  Callrate– SNPwithcallrate<0.90–  Individualswithcallrate<0.90

•  Monomorphic– ExcludemonomorphicSNP.ONLYwhenMAF0

QualitycontrolBydefaultexclude(cont)

•  Parent-progenyconflicts(SNP&Individuals)– Exclusion->oppositehomozygous– ForSNP:>10%ofparent-progenyexclusionfromthetotal ofpairsevaluated

– ForIndividuals:>1%ofparent-progenyfromtotalnumberofSNP

Controldefaultvalues

•  ForMAF– OPTIONminfreqx

•  Callrate– OPTIONcallratex– OPTIONcallrateAnimx

•  Mendelianconflicts– OPTIONexclusion_thresholdx– OPTIONexclusion_threshold_snpx

Parent-progenyconflicts

•  Presenceoftheseconflictsresultsinanega@veHmatrix!!!

•  Problemsines@ma@onofvariancecomponentbyREML,programsdoesnotconverge,etc.

•  Solu@on:–  Reportallconflicts,withcountsforeachindividualasparentorprogenytotracetheconflicts

–  Removeprogenygenotype•  maybenotthebestop@on•  Butresultsinaposi@ve-definiteHmatrix!!!

Parent-progenyconflicts

•  OPTIONverify_parentagex–  0:noac@on–  1:onlydetect –  2:detectandsearchforanalternateparent;nochangetoanyfile.Notimplemented

•  implementedinseekparen*90program–  3:detectandeliminateprogenieswithconflicts(default)

OtherOp@ons•  Exclusionofselectedchromosomes:

– OPTIONexcludeCHRn1n2n3...

•  Inclusionofselectedchromosomes:– OPTIONincludeCHRn1n2n3...

•  Excludesamplesfromanalyses

– OPTIONexcludeSamplen1n2n3

•  Informwhicharesexchromosomes:– OPTIONsex_chrn–  Chromosome#>nwillbeexcludedonlyforHWEandparent-progenychecks,butnotincalcula@ons

SNPmapfile•  OPTIONchrinfo•  Forsomegenomicanalyses(GWAS)orQC

•  Format:–  SNPnumber

•  IndexnumberofSNPinthesortedmapbychromosomeandposi@on

–  chromosomenumber–  Posi@on–  SNPname(Op@onal)

•  FirstrowcorrespondstofirstcolumnSNPingenotypefile!!!

Saving‘clean’files•  SNPexcludedfromQCaresetasmissing(i.e.Code=5)•  ExcludedIndividualsaretreatedasunrealatedinGandA22

–  ForindividualiG[i,:]=0;G[:,i]=0;G[i,i]=1;SameforA22soG-A22willcancelout

•  OPTIONsaveCleanSNPs•  SavecleangenotypedatawithexcludedSNPandindividuals

–  ForexampleforaSNP_filegt–  Cleanfleswillbe:

•  gt_clean•  gt_clean_XrefID

–  Removedwillbeoutputinfiles:•  gt_SNPs_removed•  gt_Animals_removed

Inspec@onofDiagonalofG

¨  HighdiagonalelementsfromG¤ Mislabedsamples,individualsfromotherpopula@ons/lines

¤ Problemswithsample,lowcallrate

¤ Bydefaultvalues>1.6areexcludedfromanalysis,Thresholdcanbechangedwith:

OPTIONthreshold_diagonal_gxSimeoneetal.,2011JABG

Poten@alduplicatesamples•  Allsamplesarecheckedwitheachotherusingvaluesfromgenomic

rela@onshipmatrix–  x=G(i,j)/sqrt(G(i,i),G(j,j))

–  Valuesofx>0.90areprintedintheoutput

•  Thresholdtoiden@fypoten@alduplicates

–  OPTIONthreshold_duplicate_samplesx

•  Excludespecificsamples–  OPTIONexcludeSamplen1n2….

Correla@onoff-diagonalGvsA•  Computecorrela@onforallelementsofA>0.02•  Poten@alproblemswithmatchinggenotypefileandpedigree

file•  Forlowvalues(printawarning!!!!•  Forlowvalues(programstop!!!•  Ifs@llyouwanttogo…

–  OPTIONthrStopCorAG-1

Lowoff-diagonalcorrela@onHalf-sibscontemporarygroup

OppositeHomozygousOff-diagonalGvsA22

Correla@onoff-diagonal0.47

Lookingforstra@fica@oninpopula@ons

•  OPTIONplotpca–  (onlypreGSf90notinapplica@on

programs)

–  Plotthefirst2PC•  OPTIONextra_info_pcafilenamecol

–  Filewithvariables(alphanumeric)toplotPCwithdifferentcolorsfordifferentclasses

–  Sameorderasgenotypefile

LDcalcula@onandop@ons

NoQualitycontrol

•  ONLYuse:–  IfQCwasperformedinapreviousrun– and“clean”genotypefileisused

•  OPTIONno_quality_control

Op@onsforBlendingGandA•  OPTIONAlphaBetaalphabeta

–  G=alpha*Gr+beta*A

•  OPTIONtunedG–  0:noadjustment–  1:mean(diag(G))=1,mean(offdiag(G))=0–  2:mean(diag(G))=mean(diag(A)),mean(offdiag(G))=mean(offdiag(A))(default)–  3:mean(G)=mean(A)–  4:UseFstadjustment.Powelletal.(2010)&Vitezicaetal.(2011)

Useinapplica@onprograms

•  Userenumf90forproperrenumeringandcrea@onofcrossreferenceidandparameterfile

•  Iflargenumberofgenotypes– Precomputeinv(G)-inv(A22)(PreGSF90)– ModifyparameterfiletoreadGimA22i– BLUPF90,AIREMLF90,GIBBSxF90….

•  Generallyallstepscanbeinascriptfiletofacilitaterunningprograms

PreGSf90wiki

seekparen}90

•  Programtocheckandassignpaternityusinggenomicinforma@on

•  Detectparent-offspringincompa@bili@esbasedoncountsofconflicts(oppositehomzygousOHM)– Hayes2010JAS– Wiggansetal2010JDS

Paternitycheck

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Genotype codes: 0 Homozygous 1 Heterozygous

2 Homozygous 5 NoCall

Missing dam genotype 3 putatives sires Assumption that 1 conflict is genotyping error

Sire Candidates

Progeny

seekparen}90

seekparen}90•  Mul@pleSNPChips

--chips

•  SNPFile

seekparen}90

•  Exclusion/inclusionSNP– ListofSNPnamestobeexcludedorincludedinparentagetes@ng

--exclude_snp--include_snp

•  Callrate--thr_call_rate

OutputfilesParent_Conflicts_Stat

Check_Parent_Pedigree.txt

Seek_Sire.txt