apt-probeset-genotype \
-o /data/outbred_jerome/ANALYSIS/all_F1_MvA_005 \
-c /data/outbred_jerome/ANALYSIS/MOUSEDIVm520650.CDF \
--cel-files /data/outbred_jerome/ANALYSIS/all_f1s_cels_liste.txt \
-s /data/outbred_jerome/ANALYSIS/SNPsubset.txt \
--a quant-norm.sketch=50000,pm-only,brlmm-p.CM=1.bins=100.mix=1.bic=2.HARD=3.SB=0.75.KX=0.2.KH=0.3.KXX=-0.1.KAH=-0.1.KHB=-0.1.transform=MVA.AAM=2.0.BBM=-2.0.AAV=0.06.BBV=0.06.ABV=0.06.copyqc=0.00000.wobble=0.05.CSepThr=4.CSepPen=0.1.KYAH=-0.05.KYHB=-0.05.KYAB=-0.1.AAY=9.ABY=9.5.BBY=9.copytype=-1.clustertype=2.ocean=0.00001.MS=0.05 \
--read-models-brlmmp /data/outbred_jerome/ANALYSIS/Mouse.models \
--summaries \
--write-models \
--chrX-probes /data/outbred_jerome/ANALYSIS/Mouse.chrXprobes \
--chrY-probes /data/outbred_jerome/ANALYSIS/Mouse.chrYprobes \
--special-snps /data/outbred_jerome/ANALYSIS/Mouse.specialSNPs