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etal / cnvkit

Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
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Segmentation result dubious? #690

Open marchoeppner opened 2 years ago

marchoeppner commented 2 years ago

Hi,

I am still fighting with this tool to get a reliable workflow sorted out. I am now doing this very slowly, by hand - against a chip-validated cohort.

I am now a bit confused about the segmentation results, which I understand bin regions into consistent regions of gain/loss/normal.

The following example:

My "normal" reference from 150 exomes:

chr1 152600675 152600851 LCE3C -0.150035 166.796 0.522727 0.374282 chr1 152600896 152601016 LCE3C -0.0925092 119.702 0.658333 0.377151

My sample CNR file:

chr1 152600675 152600851 LCE3C -26.7574 0 0.870625 chr1 152600896 152601016 LCE3C -26.0326 0 0.867989

My sample CNS file (doesn't really change based on "-m" chosen:

chr1 152350847 152760760 FLG-AS1,FLG2,CRNN,LCE5A,CRCT1,LCE3E,LCE3D,LCE3C,LCE3B,LCE3A,LCE2D,LCE2C,LCE2B,LCE2A,LCE4A,C1orf68,KPRP -0.947646 152.428 97 92.5902

This particular gene is deleted in my sample, which is also suggested by the coverage measured (i.e. 0) as well as by the analysis with the CNV chip... yet the segmentation bins it together with several other genes that all have "normal" coverage (i.e. around 100X).

Any idea why?

Data set: exomes (idt xGen), 2*150bp on a Novaseq Processing: Alignment with bwa, duplicate-marking with samtools

tetedange13 commented 2 years ago

Hi @marchoeppner ,

I may help you a bit. You mention "-m" parameter, I guess the one from batch command ? => If so, an alias for this parameter is --seq-method, meaning you have to specify enrichment method matching your NGS wetlab kit (possible values are: "hybrid", "wgs" or "amplicon") => As xGen IDT looked like and hybrid-capture kit, I think "-m hybrid" is the one for you (also the default value used by CNVkit, so you could leave this parameter unset)

If default segmentation method (called "CBS") does not give you proper results, maybe you should rather try a different --segment-method param (still on batch command) => I personally find "HAAR" method is performing well on tumor data

If this is not helping you, several ideas:

Have a nice day. Kind regards, Felix.

etal commented 2 years ago

If the gene has only 2 exons, then that may not be enough data points for the segmentation methods to pick it up as a distinct region. At that point you can try a smaller bin size, or use bintest to try to pick out significant deviations of each exon.

Felix's tips are also good. Thanks!

marchoeppner commented 2 years ago

Apologies for the late reply.

This is the bintest file around the locus in question:

chr1    113391229       113391349       MAGI3   95.375  0.625269        0.979203        0.00205135
chr1    121324454       121324669       SRGAP2C 286.972 0.427088        0.989408        0.00386882
chr1    145836466       145836586       POLR3C  52.15   -0.682782       0.978912        0.00052633
chr1    145872155       145872275       ANKRD35 27.375  -1.02666        0.970942        6.90499e-07
chr1    149926798       149926918       SF3B4   77.0667 -0.596516       0.982707        0.00101389
chr1    150076875       150076995       VPS45   54.9917 -0.768839       0.982161        3.23904e-06
chr1    150949084       150949300       SETDB1  75.3796 -0.508575       0.984915        0.00397984
chr1    150995230       150995350       ANXA9   44.4833 -0.705897       0.981252        7.21164e-05
chr1    151046061       151046181       BNIPL   49.05   -0.61031        0.977816        0.00456865
chr1    151134779       151134899       SEMA6C  50.4917 -0.611552       0.979174        0.00289377
chr1    151287456       151287576       ZNF687  61.4833 -0.633461       0.98538 4.8074e-05
chr1    151345883       151346003       RFX5    62.1083 -0.519786       0.98431 0.00387047
chr1    151708971       151709091       CELF3   44.7667 -0.740082       0.974456        0.000700445
chr1    151763301       151763421       MRPL9,OAZ3      104.225 0.514058        0.985548        0.00252936
chr1    152600675       152600851       LCE3C   0       -26.7369        0.870625        0
chr1    152600896       152601016       LCE3C   0       -26.0121        0.867989        0
chr1    152613810       152613930       LCE3B   0       -26.1767        0.865374        0
chr1    152613965       152614098       LCE3B   0       -25.7883        0.845185        0
chr1    153948560       153948680       CRTC2   73.3083 -0.525346       0.984191        0.00352422
chr1    154936577       154936697       PMVK    39.2    -0.80381        0.975793        6.82269e-05
chr1    155182029       155182149       TRIM46  57.9167 -0.521404       0.986182        0.00144601
chr1    156081782       156082030       MEX3A   93.754  0.592654        0.982282        0.00136359
chr1    156334700       156334820       CCT3    40.25   -0.74676        0.975979        0.0003262
chr1    156468170       156468290       MEF2D   15.8917 -0.877444       0.965103        0.000535568
chr1    156476991       156477111       MEF2D   49.5667 -0.743115       0.984495        9.56101e-07
chr1    156477117       156477237       MEF2D   56.125  -0.602785       0.979539        0.00312764
chr1    156625281       156625401       HAPLN2  20.9833 -0.907126       0.969699        5.49555e-05
chr1    156670531       156670651       NES     32.475  -0.700428       0.970868        0.00446943

And this is the cnr file:

chr1    152357391       152357511       FLG-AS1,FLG2    135.883 0.0895122       0.974854
chr1    152357526       152357701       FLG-AS1,FLG2    148.343 0.0978992       0.987287
chr1    152358724       152358921       FLG-AS1,FLG2    129.203 0.106038        0.989793
chr1    152359421       152409093       Antitarget      0.422129        -0.195951       0.563555
chr1    152409593       152409713       CRNN    118.083 -0.00487429     0.98502
chr1    152409788       152409908       CRNN    185.042 0.283859        0.974925
chr1    152409971       152410091       CRNN    225.367 0.187979        0.980972
chr1    152410142       152410262       CRNN    260.842 0.246921        0.976006
chr1    152410317       152410437       CRNN    183.333 0.159438        0.979672
chr1    152410491       152410611       CRNN    53.7333 -0.233896       0.965312
chr1    152410661       152410781       CRNN    78.175  0.117298        0.971248
chr1    152410822       152410996       CRNN    124.73  -0.103568       0.987872
chr1    152412104       152412285       CRNN    127.519 0.178722        0.987122
chr1    152412785       152511006       Antitarget      0.189929        0.0677293       0.983919
chr1    152511506       152511704       LCE5A   128.328 -0.0465126      0.988711
chr1    152511767       152511887       LCE5A   49.3333 -0.472388       0.968157
chr1    152515563       152515683       CRCT1   31.8333 0.102195        0.960696
chr1    152516183       152565426       Antitarget      0.212985        0.305013        0.967124
chr1    152565926       152566046       LCE3E   126.783 0.237516        0.981357
chr1    152566088       152566208       LCE3E   111.783 0.0668078       0.986228
chr1    152566708       152579160       Antitarget      0.176036        0.236783        0.881214
chr1    152579660       152579780       LCE3D   112.367 -0.0285125      0.982481
chr1    152579830       152579950       LCE3D   169.217 0.0875663       0.980578
chr1    152600675       152600851       LCE3C   0       -26.7577        0.870625
chr1    152600896       152601016       LCE3C   0       -26.0329        0.867989
chr1    152601516       152613310       Antitarget      0       -16.6334        0.481387
chr1    152613810       152613930       LCE3B   0       -26.1975        0.865374
chr1    152613965       152614098       LCE3B   0       -25.8091        0.845185
chr1    152622833       152622953       LCE3A   99.2667 0.245872        0.981987
chr1    152622993       152623113       LCE3A   164.05  0.260084        0.979543
chr1    152623613       152663603       Antitarget      0.507552        0.191116        0.691695
chr1    152664103       152664223       LCE2D   150.617 -0.0394747      0.986341
chr1    152664309       152664429       LCE2D   121.833 -0.339225       0.980542
chr1    152664929       152675515       Antitarget      0.110901        -0.67058        0.884075
chr1    152676015       152676135       LCE2C   174.325 -0.0332495      0.986333
chr1    152676220       152676340       LCE2C   155.192 0.134614        0.981805
chr1    152676840       152686341       Antitarget      0.213451        0.310819        0.886409
chr1    152686841       152686961       LCE2B   167     0.153842        0.985815
chr1    152687047       152687167       LCE2B   166.325 0.0898229       0.984911
chr1    152687667       152698404       Antitarget      0.19186 0.359983        0.859183
chr1    152698904       152699024       LCE2A   168.975 0.180072        0.984163
chr1    152699093       152699213       LCE2A   189.258 0.228655        0.985887

And the CNS file :

chromosome      start   end     gene    log2    cn      depth   p_ttest probes  weight
chr1    69093   125165731       OR4F5,OR4F3,OR4F16,OR4F29,OR4F3,OR4F29,OR4F16,SAMD11,NOC2L,KLHL17,PLEKHN1,PERM1,HES4,ISG15,AGRN,C1orf159,TTLL10,TNFRSF18,TNFRSF4,SDF4,C1QTNF12,UBE2J2,SCNN1D,ACAP3,ACAP3,MIR6726,PUSL1,INTS11,INTS11,MIR6727,CPTP,TAS1R3,DVL1,DVL1,MIR6808,MXRA8,AURKAIP1,CCNL2,MRPL20,ANKRD65,TMEM88B,VWA1,ATAD3C,ATAD3B,ATAD3A,TMEM240,SSU72,FNDC10,MIB2,MMP23B,MMP23A,CDK11B,SLC35E2B,CDK11A,SLC35E2A,NADK,GNB1,CALML6,TMEM52,CFAP74,GABRD,PRKCZ,PRKCZ,FAAP20,FAAP20,FAAP20,LOC112268219,SKI,MORN1,RER1,PEX10,PLCH2,PANK4,HES5,TNFRSF14-AS1,TNFRSF14,TNFRSF14,PRXL2B,PRXL2B,MMEL1,MMEL1,TTC34,ACTRT2,PRDM16,ARHGEF16,MEGF6,TPRG1L,WRAP73,TP73,CCDC27,SMIM1,LRRC47,CEP104,DFFB,C1orf174,AJAP1,NPHP4,KCNAB2,CHD5,RPL22,RNF207,ICMT,HES3,GPR153,ACOT7,HES2,ESPN,TNFRSF25,PLEKHG5,NOL9,TAS1R1,ZBTB48,KLHL21,PHF13,THAP3,DNAJC11,CAMTA1,VAMP3,PER3,UTS2,TNFRSF9,PARK7,ERRFI1,SLC45A1,RERE,ENO1,CA6,SLC2A7,SLC2A5,GPR157,H6PD,SPSB1,SLC25A33,TMEM201,PIK3CD,CLSTN1,CTNNBIP1,LZIC,NMNAT1,RBP7,UBE4B,KIF1B,PGD,CENPS,CENPS-CORT,CENPS-CORT,CORT,DFFA,PEX14,CASZ1,C1orf127,TARDBP,MASP2,SRM,EXOSC10,EXOSC10,EXOSC10-AS1,MTOR,MTOR,MTOR-AS1,MTOR,ANGPTL7,UBIAD1,DISP3,FBXO2,FBXO44,FBXO6,MAD2L2,DRAXIN,AGTRAP,C1orf167,C1orf167,C1orf167-AS1,C1orf167,MTHFR,MTHFR,CLCN6,NPPA-AS1,NPPA,NPPB,KIAA2013,PLOD1,MFN2,MIIP,MIIP,MIR6729,TNFRSF8,TNFRSF1B,TNFRSF1B,MIR4632,VPS13D,DHRS3,DHRS3,MIR6730,AADACL4,AADACL3,C1orf158,PRAMEF12,PRAMEF1,PRAMEF11,HNRNPCL1,PRAMEF2,PRAMEF2,PRAMEF4,PRAMEF10,PRAMEF10,PRAMEF7,PRAMEF6,PRAMEF27,PRAMEF27,HNRNPCL3,HNRNPCL4,PRAMEF26,PRAMEF25,HNRNPCL2,PRAMEF25,PRAMEF26,HNRNPCL4,HNRNPCL3,PRAMEF27,PRAMEF9,PRAMEF13,PRAMEF18,PRAMEF22,PRAMEF5,PRAMEF8,PRAMEF33,PRAMEF15,PRAMEF14,PRAMEF19,PRAMEF17,PRAMEF20,LRRC38,PDPN,PRDM2,KAZN,KAZN,TMEM51-AS1,TMEM51,C1orf195,TMEM51,FHAD1,FHAD1,FHAD1-AS1,EFHD2,CTRC,CELA2A,CELA2B,CASP9,DNAJC16,AGMAT,DDI2,DDI2,RSC1A1,PLEKHM2,SLC25A34,SLC25A34-AS1,TMEM82,FBLIM1,UQCRHL,FLJ37453,SPEN,SPEN,ZBTB17,SRARP,HSPB7,CLCNKA,CLCNKB,FAM131C,EPHA2,ARHGEF19,CPLANE2,FBXO42,SZRD1,SPATA21,NECAP2,NBPF1,MST1L,CROCC,MFAP2,ATP13A2,SDHB,PADI2,PADI1,PADI3,PADI4,PADI6,RCC2,ARHGEF10L,ACTL8,IGSF21,KLHDC7A,PAX7,TAS1R2,ALDH4A1,ALDH4A1,MIR4695,IFFO2,UBR4,EMC1-AS1,EMC1,EMC1,MRTO4,AKR7L,AKR7A3,AKR7A2,SLC66A1,CAPZB,MICOS10,MICOS10-NBL1,MICOS10-NBL1,NBL1,HTR6,TMCO4,RNF186,OTUD3,PLA2G2E,PLA2G2A,PLA2G5,PLA2G2D,PLA2G2F,PLA2G2C,UBXN10,VWA5B1,CAMK2N1,MUL1,FAM43B,CDA,PINK1,PINK1,PINK1-AS,DDOST,KIF17,SH2D5,HP1BP3,EIF4G3,ECE1,NBPF3,ALPL,RAP1GAP,USP48,LDLRAD2,LDLRAD2,HSPG2,HSPG2,CELA3B,CELA3A,CDC42,WNT4,ZBTB40,EPHA8,C1QA,C1QC,C1QB,EPHB2,EPHB2,MIR4253,LACTBL1,TEX46,KDM1A,LUZP1,HTR1D,HNRNPR,ZNF436,TCEA3,ASAP3,E2F2,E2F2,LOC101928163,ID3,MDS2,RPL11,ELOA,PITHD1,LYPLA2,GALE,HMGCL,FUCA1,CNR2,PNRC2,SRSF10,MYOM3,IL22RA1,IFNLR1,GRHL3,GRHL3,STPG1,STPG1,NIPAL3,RCAN3,NCMAP,SRRM1,CLIC4,RUNX3,SYF2,RSRP1,RSRP1,RHD,TMEM50A,RHCE,MACO1,LDLRAP1,MAN1C1,SELENON,MTFR1L,LOC646471,MTFR1L,MTFR1L,AUNIP,AUNIP,PAQR7,STMN1,PAFAH2,EXTL1,SLC30A2,TRIM63,PDIK1L,FAM110D,ZNF593,CNKSR1,CATSPER4,CEP85,SH3BGRL3,UBXN11,UBXN11,CD52,CD52,CRYBG2,ZNF683,LIN28A,DHDDS,HMGN2,RPS6KA1,RPS6KA1,MIR1976,ARID1A,PIGV,ZDHHC18,SFN,GPN2,GPATCH3,NR0B2,NUDC,KDF1,TENT5B,SLC9A1,WDTC1,TMEM222,SYTL1,MAP3K6,FCN3,CD164L2,GPR3,WASF2,AHDC1,FGR,IFI6,FAM76A,STX12,PPP1R8,THEMIS2,RPA2,SMPDL3B,XKR8,EYA3,PTAFR,DNAJC8,ATP5IF1,SESN2,MED18,PHACTR4,RCC1,TRNAU1AP,RAB42,TAF12,GMEB1,YTHDF2,OPRD1,EPB41,TMEM200B,SRSF4,MECR,PTPRU,MATN1,MATN1,MATN1-AS1,LAPTM5,SDC3,PUM1,NKAIN1,SNRNP40,ZCCHC17,FABP3,SERINC2,TINAGL1,HCRTR1,PEF1,COL16A1,ADGRB2,SPOCD1,PTP4A2,KHDRBS1,TMEM39B,KPNA6,TXLNA,CCDC28B,IQCC,DCDC2B,DCDC2B,TMEM234,TMEM234,TMEM234,EIF3I,EIF3I,FAM167B,LCK,HDAC1,MARCKSL1,TSSK3,BSDC1,ZBTB8B,ZBTB8A,ZBTB8OS,RBBP4,RBBP4,SYNC,SYNC,KIAA1522,YARS1,S100PBP,FNDC5,HPCA,TMEM54,RNF19B,AK2,AZIN2,TRIM62,ZNF362,A3GALT2,PHC2,PHC2,MIR3605,PHC2,PHC2-AS1,ZSCAN20,CSMD2,CSMD2,HMGB4,C1orf94,GJB5,GJB4,GJB3,GJA4,SMIM12,DLGAP3,TMEM35B,ZMYM6,ZMYM1,SFPQ,ZMYM4,ZMYM4,ZMYM4-AS1,KIAA0319L,NCDN,TFAP2E,PSMB2,C1orf216,CLSPN,AGO4,AGO1,AGO3,TEKT2,ADPRS,COL8A2,TRAPPC3,MAP7D1,THRAP3,SH3D21,EVA1B,STK40,LSM10,OSCP1,MRPS15,CSF3R,GRIK3,ZC3H12A,ZC3H12A,MIR6732,MEAF6,SNIP1,DNALI1,DNALI1,GNL2,GNL2,RSPO1,C1orf109,CDCA8,EPHA10,MANEAL,YRDC,C1orf122,MTF1,INPP5B,SF3A3,FHL3,UTP11,POU3F1,RRAGC,MYCBP,GJA9-MYCBP,GJA9-MYCBP,LOC105378663,GJA9,RHBDL2,AKIRIN1,NDUFS5,MACF1,MACF1,KIAA0754,BMP8A,BMP8A,PPIEL,PABPC4,PABPC4,PABPC4-AS1,HEYL,NT5C1A,HPCAL4,PPIE,PPIE,BMP8B,BMP8B,BMP8B,OXCT2,TRIT1,MYCL,MFSD2A,CAP1,CAP1,PPT1,PPT1,RLF,TMCO2,ZMPSTE24,COL9A2,SMAP2,ZFP69B,ZFP69,EXO5,ZNF684,RIMS3,NFYC,KCNQ4,CTPS1,SLFNL1-AS1,SLFNL1,SLFNL1-AS1,SCMH1,SCMH1,FOXO6,EDN2,HIVEP3,GUCA2B,GUCA2A,FOXJ3,RIMKLA,ZMYND12,CCDC30,PPCS,CCDC30,PPIH,YBX1,CLDN19,P3H1,C1orf50,TMEM269,SVBP,ERMAP,ZNF691,SLC2A1,FAM183A,EBNA1BP2,EBNA1BP2,MIR6733,EBNA1BP2,CFAP57,CFAP57,TMEM125,C1orf210,TIE1,MPL,CDC20,ELOVL1,ELOVL1,MIR6734,MED8,SZT2,SZT2,SZT2-AS1,SZT2,SZT2-AS1,MIR6735,SZT2,HYI,PTPRF,KDM4A,KDM4A,KDM4A-AS1,ST3GAL3,ARTN,IPO13,DPH2,ATP6V0B,B4GALT2,CCDC24,SLC6A9,KLF17,KLF18,DMAP1,ERI3,RNF220,TMEM53,ARMH1,KIF2C,RPS8,BEST4,PLK3,TCTEX1D4,BTBD19,PTCH2,EIF2B3,HECTD3,UROD,ZSWIM5,HPDL,MUTYH,MUTYH,TOE1,TOE1,TESK2,CCDC163,MMACHC,MMACHC,PRDX1,PRDX1,AKR1A1,NASP,CCDC17,GPBP1L1,TMEM69,TMEM69,IPP,IPP,MAST2,PIK3R3,P3R3URF-PIK3R3,P3R3URF-PIK3R3,TSPAN1,P3R3URF,TSPAN1,POMGNT1,POMGNT1,LURAP1,RAD54L,RAD54L,LRRC41,LRRC41,UQCRH,NSUN4,FAAH,DMBX1,MKNK1-AS1,KNCN,MKNK1-AS1,MKNK1,MKNK1,MOB3C,ATPAF1,TEX38,EFCAB14-AS1,EFCAB14,EFCAB14,CYP4B1,CYP4A11,CYP4X1,CYP4Z1,CYP4A22,PDZK1IP1,TAL1,STIL,CMPK1,FOXD2,TRABD2B,SLC5A9,SPATA6,AGBL4,AGBL4,BEND5,ELAVL4,DMRTA2,FAF1,CDKN2C,C1orf185,RNF11,TTC39A,EPS15,OSBPL9,NRDC,NRDC,MIR761,RAB3B,TXNDC12,TXNDC12,KTI12,BTF3L4,ZFYVE9,CC2D1B,ORC1,PRPF38A,TUT4,GPX7,SHISAL2A,COA7,ZYG11B,ZYG11A,ECHDC2,SCP2,PODN,SLC1A7,CPT2,CZIB,MAGOH,LRP8,DMRTB1,GLIS1,NDC1,YIPF1,DIO1,HSPB11,LRRC42,LDLRAD1,TMEM59,TCEANC2,CDCP2,CYB5RL,MRPL37,SSBP3,ACOT11,ACOT11,FAM151A,MROH7,MROH7-TTC4,MROH7-TTC4,TTC4,PARS2,TTC22,LEXM,DHCR24,TMEM61,BSND,PCSK9,USP24,PLPP3,PRKAA2,FYB2,C8A,C8B,DAB1,DAB1,OMA1,TACSTD2,MYSM1,JUN,FGGY,HOOK1,CYP2J2,C1orf87,NFIA,TM2D1,PATJ,L1TD1,KANK4,USP1,DOCK7,DOCK7,ANGPTL3,ATG4C,FOXD3-AS1,FOXD3,ALG6,ITGB3BP,EFCAB7,PGM1,ROR1,UBE2U,CACHD1,RAVER2,JAK1,AK4,DNAJC6,LEPR,LEPROT,LEPR,PDE4B,SGIP1,TCTEX1D1,INSL5,DNAI4,MIER1,SLC35D1,C1orf141,IL23R,IL12RB2,SERBP1,GADD45A,GNG12,GNG12-AS1,DIRAS3,GNG12-AS1,WLS,WLS,RPE65,DEPDC1,DEPDC1,DEPDC1-AS1,LRRC7,LRRC40,SRSF11,ANKRD13C,HHLA3,CTH,PTGER3,PTGER3,ZRANB2-AS1,ZRANB2-AS1,ZRANB2,ZRANB2,NEGR1,LRRIQ3,FPGT,FPGT-TNNI3K,FPGT-TNNI3K,TNNI3K,FPGT-TNNI3K,TNNI3K,LRRC53,ERICH3,ERICH3,ERICH3-AS1,CRYZ,CRYZ,TYW3,TYW3,LHX8,SLC44A5,ACADM,RABGGTB,MSH4,ASB17,ST6GALNAC3,ST6GALNAC5,PIGK,AK5,ZZZ3,USP33,MIGA1,NEXN,FUBP1,DNAJB4,GIPC2,PTGFR,IFI44L,IFI44,ADGRL4,ADGRL2,TTLL7,PRKACB,SAMD13,DNASE2B,RPF1,GNG5,SPATA1,SPATA1,CTBS,CTBS,SSX2IP,LPAR3,MCOLN2,MCOLN3,DNAI3,SYDE2,C1orf52,BCL10,BCL10,LOC646626,DDAH1,CCN1,ZNHIT6,COL24A1,ODF2L,CLCA2,CLCA1,CLCA4,CLCA4,CLCA4-AS1,SH3GLB1,SELENOF,HS2ST1,LINC02801,LMO4,PKN2-AS1,PKN2,PKN2,GTF2B,KYAT3,KYAT3,RBMXL1,GBP3,GBP1,GBP2,GBP7,GBP4,GBP5,GBP6,LRRC8B,LRRC8C,LRRC8D,ZNF326,BARHL2,ZNF644,HFM1,CDC7,TGFBR3,BRDT,EPHX4,SETSIP,BTBD8,C1orf146,GLMN,RPAP2,GFI1,EVI5,RPL5,RPL5,DIPK1A,DIPK1A,MTF2,TMED5,CCDC18,DR1,FNBP1L,BCAR3,BCAR3,BCAR3-AS1,DNTTIP2,GCLM,ABCA4,ARHGAP29,ABCD3,F3,SLC44A3,CNN3,CNN3,CNN3-DT,ALG14,ALG14,ALG14-AS1,TLCD4,TLCD4-RWDD3,TLCD4,TLCD4-RWDD3,LOC101928118,TLCD4-RWDD3,LOC101928118,TLCD4-RWDD3,RWDD3,RWDD3,PTBP2,DPYD,DPYD,DPYD-AS1,SNX7,PLPPR5,PLPPR4,MIR548N,PALMD,MIR548N,FRRS1,FRRS1,AGL,SLC35A3,MFSD14A,SASS6,TRMT13,TRMT13,LRRC39,LRRC39,DBT,RTCA,CDC14A,GPR88,VCAM1,EXTL2,SLC30A7,DPH5,S1PR1,OLFM3,COL11A1,LOC101928436,RNPC3,AMY2B,AMY2A,AMY1C,AMY1A,AMY1B,PRMT6,NTNG1,VAV3,VAV3,VAV3-AS1,SLC25A24,NBPF4,NBPF6,FAM102B,HENMT1,PRPF38B,FNDC7,STXBP3,AKNAD1,GPSM2,GPSM2,CLCC1,CLCC1,WDR47,TAF13,TMEM167B,C1orf194,ELAPOR1,SARS1,CELSR2,PSRC1,MYBPHL,SORT1,PSMA5,SYPL2,ATXN7L2,CYB561D1,AMIGO1,GPR61,GNAI3,GNAT2,AMPD2,GSTM4,GSTM2,GSTM5,GSTM3,EPS8L3,CSF1,AHCYL1,STRIP1,ALX3,UBL4B,SLC6A17,KCNC4,RBM15,SLC16A4,LAMTOR5,LAMTOR5,LAMTOR5-AS1,PROK1,KCNA10,KCNA2,KCNA3,CD53,LRIF1,DRAM2,CEPT1,DENND2D,CHI3L2,CHIA,PIFO,OVGP1,WDR77,ATP5PB,C1orf162,TMIGD3,TMIGD3,ADORA3,TMIGD3,RAP1A,RAP1A,INKA2,DDX20,KCND3,LINC01750,CTTNBP2NL,WNT2B,WNT2B,ST7L,ST7L,CAPZA1,MOV10,RHOC,PPM1J,TAFA3,SLC16A1,LRIG2,MAGI3,PHTF1,RSBN1,AP4B1-AS1,PTPN22,AP4B1-AS1,BCL2L15,AP4B1-AS1,AP4B1,AP4B1,AP4B1,DCLRE1B,DCLRE1B,HIPK1,OLFML3,SYT6,TRIM33,BCAS2,DENND2C,AMPD1,NRAS,CSDE1,SIKE1,SYCP1,TSHB,TSPAN2,NGF-AS1,NGF,VANGL1,CASQ2,NHLH2,SLC22A15,MAB21L3,ATP1A1,ATP1A1,ATP1A1-AS1,CD58,IGSF3,LINC02868,CD2,PTGFRN,CD101,CD101,LOC101929099,TTF2,TRIM45,VTCN1,MAN1A2,TENT5C,GDAP2,WDR3,WDR3,SPAG17,SPAG17,TBX15,WARS2,WARS2,WARS2-AS1,HAO2,HSD3B2,HSD3B1,ZNF697,PHGDH,HMGCS2,REG4,NBPF7,ADAM30,NOTCH2,SEC22B,NBPF8,NBPF26,PPIAL4A,H3P4,FCGR1B,H3P4,FCGR1B,LOC100996318,FAM72B,SRGAP2C,SRGAP2C,SRGAP2-AS1       -0.0204693      2       94.9849 1.75154e-48       15198   14707.9
chr1    143277361       152515683       LINC02591,LOC644634,H3-2,FAM72C,FAM72C,SRGAP2D,PPIAL4F,PPIAL4E,PPIAL4D,NBPF15,SRGAP2-AS1,SRGAP2B,SRGAP2B,SRGAP2B,FAM72D,FAM72D,FAM72C,LINC01145,LOC644634,NBPF20,GPR89A,PDZK1,CD160,RNF115,POLR3C,NUDT17,PIAS3,PIAS3,MIR6736,ANKRD35,ITGA10,PEX11B,RBM8A,RBM8A,LIX1L-AS1,LIX1L-AS1,LIX1L,LIX1L,ANKRD34A,POLR3GL,TXNIP,HJV,NBPF10,NOTCH2NLA,NBPF12,PRKAB2,CHD1L,FMO5,CHD1L,BCL9,ACP6,GJA5,GJA8,GPR89B,NBPF11,PPIAL4G,NBPF14,NUDT4P2,NUDT4B,PDE4DIP,PDE4DIP,LOC653513,NBPF9,NBPF19,PPIAL4C,H2BC18,FCGR1A,H2BC18,H3C13,H4C15,H4C14,H3C15,H3C14,H2AC18,H2AC19,H2AC19,H2AC18,H3C14,H3C15,H2BC21,H2AC20,H2AC21,BOLA1,SV2A,SF3B4,MTMR11,OTUD7B,VPS45,PLEKHO1,ANP32E,CA14,APH1A,C1orf54,CIART,MRPS21,PRPF3,RPRD2,TARS2,TARS2,MIR6878,ECM1,ADAMTSL4,MCL1,ENSA,GOLPH3L,HORMAD1,CTSS,CTSK,ARNT,SETDB1,CERS2,ANXA9,MINDY1,PRUNE1,BNIPL,C1orf56,CDC42SE1,MLLT11,GABPB2,SEMA6C,TNFAIP8L2,TNFAIP8L2-SCNM1,TNFAIP8L2-SCNM1,LYSMD1,TNFAIP8L2-SCNM1,SCNM1,TNFAIP8L2-SCNM1,SCNM1,TMOD4,TMOD4,VPS72,PIP5K1A,PSMD4,ZNF687,PI4KB,RFX5,SELENBP1,PSMB4,POGZ,CGN,TUFT1,SNX27,CELF3,RIIAD1,MRPL9,MRPL9,OAZ3,OAZ3,TDRKH,LINGO4,RORC,C2CD4D,C2CD4D,C2CD4D-AS1,C2CD4D-AS1,THEM5,THEM5,THEM4,S100A10,S100A11,LOC100131107,TCHHL1,TCHH,RPTN,HRNR,FLG,FLG,FLG-AS1,FLG-AS1,FLG2,CRNN,LCE5A,CRCT1 0.0399078       2       111.392 2.72082e-10       1696    1603.23
chr1    152516183       248945922       LCE3E,LCE3D,LCE3C,LCE3B,LCE3A,LCE2D,LCE2C,LCE2B,LCE2A,LCE4A,C1orf68,KPRP,LCE1F,LCE1E,LCE1D,LCE1C,LCE1B,LCE1A,LCE6A,SMCP,IVL,SPRR4,SPRR1A,SPRR3,SPRR1B,SPRR2D,SPRR2A,SPRR2B,SPRR2E,SPRR2F,SPRR2G,LELP1,PRR9,LORICRIN,PGLYRP3,PGLYRP4,S100A9,S100A12,S100A8,S100A8,S100A7A,S100A7,S100A6,S100A5,S100A4,LOC101928034,S100A3,S100A2,S100A16,S100A14,S100A13,S100A13,S100A1,CHTOP,SNAPIN,ILF2,NPR1,NPR1,MIR8083,INTS3,SLC27A3,GATAD2B,DENND4B,CRTC2,SLC39A1,SLC39A1,MIR6737,CREB3L4,JTB,RAB13,RPS27,NUP210L,TPM3,C1orf189,C1orf43,C1orf43,UBAP2L,UBAP2L,HAX1,AQP10,ATP8B2,IL6R,SHE,TDRD10,UBE2Q1,UBE2Q1,UBE2Q1-AS1,CHRNB2,ADAR,KCNN3,PMVK,PBXIP1,PYGO2,PYGO2,LOC101928120,LOC101928120,SHC1,CKS1B,FLAD1,LENEP,ZBTB7B,ZBTB7B,DCST2,DCST2,DCST1,DCST1,DCST1-AS1,DCST1-AS1,ADAM15,DCST1-AS1,EFNA4,EFNA4,EFNA3,EFNA1,SLC50A1,DPM3,KRTCAP2,TRIM46,MUC1,THBS3,MTX1,GBA,FAM189B,SCAMP3,CLK2,HCN3,PKLR,FDPS,FDPS,RUSC1-AS1,RUSC1-AS1,RUSC1,RUSC1,ASH1L,ASH1L,MIR555,MSTO1,MSTO2P,YY1AP1,DAP3,MSTO2P,GON4L,GON4L,SYT11,RIT1,KHDC4,RXFP4,ARHGEF2,ARHGEF2,MIR6738,SSR2,UBQLN4,LAMTOR2,RAB25,MEX3A,LMNA,SEMA4A,SLC25A44,PMF1,PMF1-BGLAP,PMF1-BGLAP,BGLAP,PAQR6,SMG5,SMG5,TMEM79,GLMP,VHLL,CCT3,CCT3,TSACC,TSACC,RHBG,MIR9-1HG,MEF2D,IQGAP3,TTC24,NAXE,GPATCH4,HAPLN2,BCAN,NES,CRABP2,ISG20L2,RRNAD1,MRPL24,HDGF,PRCC,SH2D2A,SH2D2A,NTRK1,NTRK1,INSRR,NTRK1,PEAR1,LRRC71,ARHGEF11,ETV3L,ETV3,FCRL5,FCRL4,FCRL3,FCRL2,FCRL1,CD5L,KIRREL1,CD1D,CD1A,CD1C,CD1B,CD1E,OR10T2,OR10K2,OR10K1,OR10R2,OR6Y1,OR6P1,OR10X1,OR10Z1,SPTA1,OR6K2,OR6K3,OR6K6,OR6N1,OR6N2,MNDA,PYHIN1,PYDC5,IFI16,IFI16,AIM2,CADM3,CADM3,CADM3-AS1,ACKR1,FCER1A,OR10J3,OR10J1,OR10J4,OR10J1,OR10J5,APCS,CRP,DUSP23,FCRL6,SLAMF8,SLAMF8,SNHG28,SNHG28,VSIG8,CFAP45,CFAP45,MIR4259,TAGLN2,IGSF9,SLAMF9,PIGM,KCNJ10,KCNJ9,IGSF8,ATP1A2,ATP1A4,CASQ1,LOC729867,PEA15,PEA15,DCAF8,PEX19,COPA,NCSTN,NHLH1,VANGL2,SLAMF6,CD84,SLAMF1,CD48,SLAMF7,LY9,CD244,ITLN1,LOC101928372,ITLN2,ITLN2,F11R,TSTD1,USF1,ARHGAP30,NECTIN4,KLHDC9,PFDN2,NIT1,NIT1,DEDD,UFC1,USP21,PPOX,B4GALT3,ADAMTS4,ADAMTS4,NDUFS2,NDUFS2,FCER1G,APOA2,TOMM40L,TOMM40L,MIR5187,TOMM40L,NR1I3,NR1I3,PCP4L1,MPZ,SDHC,SDHC,CFAP126,FCGR2A,HSPA6,FCGR3A,FCGR2C,FCGR3B,FCGR2B,FCRLA,FCRLB,DUSP12,ATF6,OLFML2B,NOS1AP,SPATA46,C1orf226,SH2D1B,UHMK1,UAP1,DDR2,HSD17B7,CCDC190,RGS4,RGS5,RGS5,RGS5-AS1,NUF2,PBX1,LMX1A,RXRG,LRRC52-AS1,LRRC52,MGST3,ALDH9A1,TMCO1,UCK2,FAM78B,POGK,TADA1,ILDR2,MAEL,GPA33,STYXL2,POU2F1,CD247,CREG1,RCSD1,MPZL1,ADCY10,MPC2,MPC2,DCAF6,DCAF6,GPR161,TIPRL,SFT2D2,TBX19,XCL2,XCL1,DPT,ATP1B1,NME7,BLZF1,BLZF1,CCDC181,CCDC181,SLC19A2,F5,SELP,SELL,SELE,METTL18,C1orf112,C1orf112,SCYL3,SCYL3,KIFAP3,METTL11B,GORAB-AS1,GORAB,GORAB,PRRX1,MROH9,FMO3,FMO2,FMO1,FMO4,PRRC2C,MYOC,VAMP4,EEF1AKNMT,DNM3,C1orf105,C1orf105,PIGC,SUCO,FASLG,TNFSF18,TNFSF4,PRDX6,SLC9C2,ANKRD45,ANKRD45,TEX50,KLHL20,CENPL,DARS2,ZBTB37,SERPINC1,RC3H1,RABGAP1L,RABGAP1L,GPR52,CACYBP,MRPS14,TNN,KIAA0040,TNR,COP1,PAPPA2,ASTN1,BRINP2,SEC16B,CRYZL2P-SEC16B,RASAL2,TEX35,RALGPS2,RALGPS2,ANGPTL1,FAM20B,TOR3A,ABL2,SOAT1,AXDND1,AXDND1,NPHS2,NPHS2,TDRD5,FAM163A,TOR1AIP2,TOR1AIP1,CEP350,QSOX1,LHX4,LHX4,LHX4-AS1,ACBD6,XPR1,KIAA1614,STX6,MR1,IER5,CACNA1E,ZNF648,GLUL,TEDDM1,RGSL1,RNASEL,RGS16,RGS8,NPL,DHX9,SHCBP1L,LAMC1,LAMC1,LAMC1-AS1,LAMC2,NMNAT2,SMG7,NCF2,ARPC5,RGL1,APOBEC4,RGL1,COLGALT2,TSEN15,C1orf21,EDEM3,NIBAN1,RNF2,TRMT1L,SWT1,IVNS1ABP,HMCN1,PRG4,PRG4,TPR,TPR,ODR4,PDC-AS1,PDC,PTGS2,PLA2G4A,BRINP3,RGS18,RGS21,RGS1,RGS13,RGS2,UCHL5,UCHL5,RO60,RO60,GLRX2,CDC73,CDC73,B3GALT2,KCNT2,CFH,CFHR3,CFHR1,CFHR4,CFHR2,CFHR5,F13B,ASPM,ZBTB41,CRB1,DENND1B,C1orf53,LHX9,NEK7,ATP6V1G3,PTPRC,NR5A2,ZNF281,KIF14,DDX59,CAMSAP2,GPR25,INAVA,KIF21B,CACNA1S,ASCL5,TMEM9,IGFN1,PKP1,TNNT2,LAD1,TNNI1,PHLDA3,CSRP1,NAV1,NAV1,IPO9-AS1,NAV1,IPO9-AS1,MIR1231,IPO9-AS1,IPO9,IPO9,IPO9,MIR6739,SHISA4,LMOD1,TIMM17A,RNPEP,RNPEP,ELF3-AS1,RNPEP,ELF3-AS1,MIR6740,ELF3,GPR37L1,ARL8A,PTPN7,LGR6,UBE2T,PPP1R12B,SYT2,KDM5B,RABIF,KLHL12,ADIPOR1,CYB5R1,TMEM183A,PPFIA4,MYOG,MYOPARR,ADORA1,MYBPH,CHI3L1,CHIT1,BTG2,FMOD,PRELP,OPTC,ATP2B4,LAX1,ZC3H11A,ZBED6,ZC3H11A,SNRPE,SOX13,ETNK2,ETNK2,ERLNC1,REN,KISS1,GOLT1A,PLEKHA6,PPP1R15B,PIK3C2B,MDM4,LRRN2,NFASC,CNTN2,TMEM81,RBBP5,DSTYK,TMCC2,NUAK2,KLHDC8A,LEMD1-AS1,LEMD1,LEMD1,CDK18,MFSD4A,ELK4,SLC45A3,NUCKS1,RAB29,SLC41A1,PM20D1,SLC26A9,SLC26A9,SLC26A9-AS1,RAB7B,CTSE,RHEX,AVPR1B,FAM72A,FAM72A,SRGAP2,SRGAP2,IKBKE,IKBKE,MIR6769B,RASSF5,EIF2D,DYRK3,MAPKAPK2,IL10,IL10,IL19,IL19,IL20,IL24,FCMR,PIGR,FCAMR,C1orf116,YOD1,PFKFB2,C4BPB,C4BPA,CD55,CR2,CR1,CR1L,CD46,CD34,PLXNA2,MIR205HG,MIR205HG,MIR205,CAMK1G,LAMB3,LAMB3,MIR4260,HSD11B1-AS1,G0S2,HSD11B1-AS1,HSD11B1,TRAF3IP3,TRAF3IP3,C1orf74,C1orf74,IRF6,UTP25,SYT14,SERTAD4,HHAT,KCNH1,RCOR3,TRAF5,RD3,SLC30A1,NEK2,LPGAT1,INTS7,DTL,PPP2R5A,PACC1,NENF,ATF3,FAM71A,BATF3,NSL1,TATDN3,SPATA45,FLVCR1,VASH2,ANGEL2,RPS6KC1,PROX1,SMYD2,PTPN14,CENPF,KCNK2,KCTD3,USH2A,USH2A,USH2A-AS2,ESRRG,GPATCH2,SPATA17,SPATA17,SPATA17-AS1,RRP15,TGFB2,TGFB2,MIR548F3,LYPLAL1,ZC3H11B,SLC30A10,EPRS1,BPNT1,IARS2,RAB3GAP2,MARK1,C1orf115,MTARC2,MTARC1,HLX-AS1,HLX,HLX,DUSP10,HHIPL2,TAF1A,MIA3,AIDA,BROX,FAM177B,DISP1,TLR5,SUSD4,CCDC185,CAPN8,CAPN2,TP53BP2,FBXO28,DEGS1,LOC101927164,NVL,NVL,CNIH4,WDR26,WDR26,MIR4742,CNIH3,DNAH14,LBR,ENAH,SRP9,EPHX1,TMEM63A,LEFTY1,PYCR2,PYCR2,MIR6741,LEFTY2,SDE2,H3-3A,H3P6,ACBD3,ACBD3,ACBD3-AS1,MIXL1,LIN9,PARP1,STUM,ITPKB,PSEN2,COQ8A,CDC42BPA,ZNF678,SNAP47,JMJD4,SNAP47,PRSS38,WNT9A,WNT3A,ARF1,MIR3620,ARF1,C1orf35,MRPL55,GUK1,GJC2,IBA57,OBSCN-AS1,OBSCN,OBSCN,TRIM11,TRIM11,MIR6742,TRIM17,H3-4,H2AW,H2BU1,RNF187,BTNL10,RHOU,RAB4A,CCSAP,ACTA1,NUP133,ABCB10,TAF5L,URB2,GALNT2,PGBD5,COG2,AGT,CAPN9,C1orf198,TTC13,ARV1,FAM89A,MIR1182,FAM89A,TRIM67,TRIM67,TRIM67-AS1,C1orf131,GNPAT,EXOC8,SPRTN,EGLN1,TSNAX-DISC1,TSNAX,TSNAX-DISC1,DISC1,TSNAX-DISC1,DISC1,DISC2,SIPA1L2,MAP10,NTPCR,PCNX2,MAP3K21,KCNK1,SLC35F3,COA6-AS1,COA6,COA6,TARBP1,IRF2BP2,TOMM20,RBM34,ARID4B,GGPS1,TBCE,TBCE,B3GALNT2,B3GALNT2,GNG4,LYST,NID1,GPR137B,ERO1B,EDARADD,LGALS8,LGALS8,HEATR1,HEATR1,ACTN2,MTR,MT1HL1,RYR2,LOC100130331,ZP4,CHRM3,FMN2,GREM2,RGS7,FH,KMO,KMO,OPN3,OPN3,OPN3,CHML,WDR64,EXO1,BECN2,MAP1LC3C,PLD5,CEP170,SDCCAG8,SDCCAG8,AKT3,AKT3,ZBTB18,C1orf100,ADSS2,CATSPERE,DESI2,COX20,HNRNPU,LOC101928068,EFCAB2,EFCAB2,KIF26B,SMYD3,TFB2M,CNST,SCCPDH,AHCTF1,ZNF695,ZNF670-ZNF695,ZNF670-ZNF695,ZNF670,ZNF669,C1orf229,ZNF124,VN1R5,ZNF496,NLRP3,OR2B11,OR2W5,GCSAML,OR2C3,GCSAML,OR2G2,OR2G3,OR13G1,OR6F1,OR14A2,OR14A2,OR14K1,OR1C1,OR14A16,OR11L1,TRIM58,OR2W3,OR2T8,OR2AJ1,OR2L13,OR2L8,OR2L13,OR2AK2,OR2L13,OR2L5,OR2L13,OR2L2,OR2L13,OR2L3,OR2L13,OR2M5,OR2M2,OR2M3,OR2M4,OR2T33,OR2T12,OR2M7,OR14C36,OR2T4,OR2T6,OR2T1,OR2T7,OR2T2,OR2T3,OR2T5,OR2G6,OR2T5,OR2T29,OR2T34,OR2T10,OR2T11,OR2T35,OR2T27,OR14I1,LYPD8,SH3BP5L,ZNF672,ZNF692,PGBD2       -0.0123671      2       98.4926 1.08852e-05     11766   11400.7

And the CNS call file line:

chr1 152516183 248945922 LCE3E,LCE3D,LCE3C,LCE3B,LCE3A,LCE2D,LCE2C,LCE2B,LCE2A,LCE4A,C1orf68,KPRP,LCE1F,LCE1E,LCE1D,LCE1C,LCE1B,LCE1A,LCE6A,SMCP,IVL,SPRR4,SPRR1A,SPRR3,SPRR1B,SPRR2D,SPRR2A,SPRR2B,SPRR2E,SPRR2F,SPRR2G,LELP1,PRR9,LORICRIN,PGLYR....