feat: Cnvkit call wrapper

bio/cnvkit/call/environment.yaml

@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - cnvkit =0.9.10

bio/cnvkit/call/meta.yaml

@@ -0,0 +1,17 @@
+name: "cnvkit call"
+description: >
+  Given segmented log2 ratio estimates (.cns), derive each segment’s absolute integer 
+  copy number. 
+url: https://cnvkit.readthedocs.io/en/stable/pipeline.html#call
+input:
+  - segments: Copy ratios (.cnr or .cns)
+  - vcf: VCF file name containing variants for calculation of b-allele frequencies
+output:
+  - segments: Output table file name (CNR-like table of segments, .cns)
+params:
+  - filter: Merge segments flagged by the specified filter(s) with the adjacent segment(s), optional
+  - purity: purity value of the tumor
+  - ploidy: Ploidy of the sample cells.
+  - extra: additional parameters that will be forwarded to cnvkit call
+authors:
+  - Patrik Smeds

bio/cnvkit/call/test/Snakefile

@@ -0,0 +1,12 @@
+rule cnvkit_call:
+    input:
+        segment="test.cns",
+        vcf="test.vcf",
+    output:
+        segment="test.call.cns",
+    log:
+        "logs/test.call.cns.log",
+    params:
+        extra = "" # optional
+    wrapper:
+        "master/bio/cnvkit/call"

bio/cnvkit/call/test/test.cns

@@ -0,0 +1,125 @@
+chromosome	start	end	gene	log2	probes	weight	depth
+chr1	10500	2421341	SSU72,PLCH2	0.134253	27	19.5922	1.10244
+chr1	2422582	2431202	PLCH2	0.448062	10	6.38648	1.37736
+chr1	2433501	18617471	PLCH2,PRDM16,NPHP4,CA6,MTOR,MFN2,LRRC38,KAZN	0.0661341	178	132.846	1.05182
+chr1	18617470	21479562	UBR4,KIF17	-0.407045	21	16.093	0.757367
+chr1	21479561	121352354	CDC42,ARID1A,PTAFR,PUM1,ZBTB8A,KIAA0319L,MYCL1,CAP1,HIVEP3,MPL,PTCH2,MUTYH,FAF1,CDKN2C,PPAP2B,DAB1,JUN,FGGY,DOCK7,JAK1,SLC35D1,LRRC7,NEGR1,FPGT-TNNI3K,AK5,MCOLN3,CLCA4,LRRC8B,EVI5,ABCA4,DPYD,COL11A1,NTNG1,CLCC1,KCND3,NRAS,WDR3,NOTCH2	-0.0213287	899	682.544	0.991427
+chr1	142535933	249240121	PDE4DIP,TXNIP,LIX1L,PEX11B,ITGA10,MCL1,CGN,LAMTOR2,SH2D2A,NTRK1,FCRL5,IFI16,FCGR3A,DDR2,MPC2,TNR,ASTN1,ABL2,CEP350,CACNA1E,LAMC1,SMG7,C1orf21,CDC73,CACNA1S,PPP1R12B,SOX13,MDM4,IKBKE,IL19,TRAF5,SMYD2,USH2A,SUSD4,PRSS38,C1orf198,TBCE,MTR,CHRM3,RGS7,SDCCAG8,AKT3,SMYD3	0.323628	954	716.9	1.25892
+chr2	10500	92267022	TPO,LINC00299,MBOAT2,HPCAL1,MYCN,C2orf43,ATAD2B,DNMT3A,BRE,ALK,TTC27,PRKD3,CYP1B1,SLC8A1,THADA,MSH2,MSH6,NRXN1,GPR75-ASB3,CCDC88A,VRK2,REL,USP34,EHBP1,ARHGAP25,SNRPG,TCF7L1	0.011528	794	601.241	1.01407
+chr2	95326670	237943201	LOC442028,DUSP2,FAM178B,AFF3,LOC100287010,NCK2,EDAR,BUB1,ANAPC1,IL36A,PAX8,DPP10,STEAP3,MAP3K2,NCKAP5,UBXN4,THSD7B,NXPH2,ARHGAP15,DKFZp686O1327,LYPD6B,STAM2,CCDC148-AS1,KCNH7,CSRNP3,LRP2,METTL8,ZAK,WIPF1,HOXD-AS2,PDE11A,SESTD1,ITGAV,ANKRD44,SF3B1,TMEM237,NBEAL1,PARD3B,NRP2,NDUFS1,IDH1,CPS1,ERBB4,SPAG16,BARD1,XRCC5,IGFBP2,PAX3,FARSB,NYAP2,COL4A4,GIGYF2,INPP5D,UGT1A8,AGAP1	-0.00117402	1196	903.678	1.00545
+chr2	237943200	242176790	HDAC4,KIF1A	-0.465657	29	22.8255	0.727227
+chr2	242176789	243188873	-	0.0799059	7	5.31941	1.06152
+chr3	60500	65409798	CNTN4,GRM7,VHL,ATP2B2,RAF1,FBLN2,NR2C2,RFTN1,PLCL2,KCNH8,NR1D2,RARB,ZCWPW2,RBMS3,TGFBR2,MLH1,ITGA9,CTNNB1,ZDHHC3,MAP4,DAG1,DOCK3,BAP1,NISCH,PBRM1,WNT5A,ARHGEF3,FHIT,ADAMTS9	-0.0147912	627	474.924	0.996131
+chr3	65409797	66579610	MAGI1	0.536554	8	6.27079	1.45616
+chr3	66579609	90168173	SUCLG2,MITF,PDZRN3,CADM2,VGLL3,EPHA3	0.0226327	209	157.932	1.02111
+chr3	93519632	95252544	-	-0.350095	16	11.2442	0.808707
+chr3	95252543	96400715	-	2.40683	9	6.76046	5.53091
+chr3	96400714	96825973	EPHA6	-0.398751	10	6.97009	0.762652
+chr3	96825972	96963168	EPHA6	3.18425	5	3.36428	9.12025
+chr3	96963667	97972088	EPHA6	2.22789	33	21.8018	4.73583
+chr3	97972087	141877242	ABI3BP,IQCB1,ADCY5,UMPS,ITGB5,MGLL,C3orf37,EPHB1,ARMC8,MRAS,ACPL2	-0.457192	347	262.526	0.734085
+chr3	141877241	197961930	ATR,TRPC1,MIR548H2,KCNAB1,IQCJ-SCHIP1,EGFEM1P,MYNN,TNIK,NLGN1,NAALADL2,KCNMB2,PIK3CA,SOX2-OT,MCF2L2,DGKG,LOC100131635,BCL6,PYDC2,FGF12,ACAP2,PAK2	-0.0185116	492	375.879	0.9934
+chr4	13322	49632814	GAK,FGFR3,STX18,SORCS2,CLNK,LOC441009,LDB2,KCNIP4,STIM2,C4orf19,TMEM156,RBM47,CNGA1	0.0268331	392	298.324	1.02661
+chr4	52660616	67655781	SCFD2,PDGFRA,KIT,KDR,EPHA5	0.0633659	212	157.563	1.05042
+chr4	67655780	179561500	UGT2A1,CDKL2,ANXA3,MAPK10,ABCG2,FAM190A,BMPR1B,STPG2,MTTP,PPP3CA,NFKB1,TET2,RPL34-AS1,ELOVL6,ANK2,SPRY1,LARP1B,MAML3,LRBA,FBXW7,KIAA0922,MARCH1,SPOCK3,PALLD,AADAT	-0.0145253	847	648.477	0.996519
+chr4	179561499	191025802	-	0.0835995	82	62.3061	1.0665
+chr5	10500	1295381	TERT	1.44032	30	20.1965	2.74749
+chr5	1295880	27758999	LPCAT1,ADCY2,FAM134B,CDH18,CDH12,CDH9	-0.438559	190	146.113	0.74419
+chr5	27758998	29725593	-	0.542628	13	10.4965	1.46849
+chr5	29725592	32111185	DROSHA	1.43184	18	13.4424	2.75829
+chr5	32111184	34935473	-	-0.290066	20	15.2251	0.865334
+chr5	34935472	43358297	WDR70,RICTOR	0.458204	103	77.9754	1.39435
+chr5	43358296	45907753	C5orf34	0.00786783	19	14.8139	1.01259
+chr5	49555073	180008136	ANKRD55,MAP3K1,PDE4D,ADAMTS6,MAST4,PIK3R1,POC5,SERINC5,SSBP2,XRCC4,RASA1,GPR98,FAM172A,MCTP1,CAST,STARD4-AS1,APC,MCC,COMMD10,DMXL1,PRR16,LOC100505841,ALDH7A1,SLC12A2,ADAMTS19,IL4,SKP1,SPOCK1,RELL2,SPRY4,ARHGAP26,LARS,JAKMIP2-AS1,CSF1R,PDGFRB,GRIA1,SGCD,NPM1,CREBRF,LOC643201,FGFR4,ZNF354C	-0.0054079	1238	938.117	1.00271
+chr5	180008635	180076603	FLT4	0.329968	33	20.5672	1.27176
+chr5	180077102	180904760	-	-0.0654238	6	4.3355	0.961004
+chr6	60500	31491427	NQO2,NRN1,ATXN1,TPMT,CDKAL1,LRRC16A	-0.0159055	240	177.13	0.994568
+chr6	31491426	32376398	DOM3Z,STK19,NOTCH4	-0.392197	49	22.6737	0.782461
+chr6	32775420	58745455	PACSIN1,MAPK14,CDKN1A,FOXP4,CCND3,XPO5,NFKBIE,SUPT3H,CYP39A1,PTCHD4,PKHD1,MLIP,ZNF451	0.0306187	318	231.29	1.02964
+chr6	61944507	171054567	EYS,OGFRL1,KCNQ5,BCKDHB,ME1,GABRR2,EPHA7,KLHL32,POU3F2,LOC728012,GRIK2,CDK19,LAMA4,ROS1,SLC35F1,RSPO3,PTPRK,SAMD3,ENPP3,PDE7B,MAP3K5,TNFAIP3,ADGB,LATS1,ESR1,RGS17,ARID1B,TMEM181,SOD2,IGF2R,SLC22A2,PARK2,PACRG	-0.0112598	1035	784.353	0.998503
+chr7	10500	6426280	CARD11,AIMP2,RAC1	0.12479	72	53.3312	1.09907
+chr7	6426779	55510241	RAC1,COL28A1,STEAP1B,HOXA3,CREB5,SCRN1,FKBP9,C7orf10,INHBA,GLI3,HECW1,CCM2,IKZF1,EGFR	-0.00717592	423	319.927	1.00155
+chr7	55510740	57938684	-	0.33604	15	9.03152	1.27525
+chr7	61657307	63386201	-	0.453069	12	6.33337	1.37799
+chr7	63386700	159128163	CCT6P3,HIP1,MAGI2,PCLO,GRM3,CROT,ABCB1,ZNF804B,GTPBP10,MTERF,CDK6,DYNC1I1,TRRAP,CYP3A5,CYP3A4,EPHB4,MUC12,SRPK2,PIK3CG,NRCAM,IMMP2L,C7orf60,MET,ASZ1,KCND2,POT1,SND1,SMO,AHCYL2,PLXNA4,EXOC4,TBXAS1,BRAF,TMEM178B,EPHB6,EPHA1-AS1,CNTNAP2,EZH2,LRRC61,PRKAG2,PTPRN2	0.00337069	1030	774.777	1.00967
+chr8	10500	17711900	DLGAP2,CSMD1,TNKS,RP1L1,FAM66D,SGCZ	0.0481852	161	117.883	1.0463
+chr8	17711899	29536110	CSGALNACT1,BIN3,PTK2B,EXTL3,DUSP4	-0.45971	146	110.218	0.734253
+chr8	29536109	43398986	MIR548O2,WRN,NRG1,GPR124,FGFR1,TACC1,ADAM32,ZMAT4	0.0571581	195	143.835	1.04609
+chr8	46950734	146303522	PRKDC,SNTG1,PXDNL,TOX,RAB2A,MYBL1,PREX2,SULF1,KCNB2,PKIA,RALYL,RUNX1T1,LINC00535,MATN2,VPS13B,FBXO43,SNX31,RIMS2,ZFPM2,CSMD3,LINC00536,MTBP,SQLE,MYC,PVT1,ADCY8,KHDRBS3,BOP1	-0.0044328	843	644.393	1.00289
+chr9	10500	5078278	SMARCA2,SLC1A1,JAK2	-0.0778313	129	98.9505	0.957546
+chr9	5078277	47317179	JAK2,PTPRD,LOC389705,BNC2,CDKN2A,CDKN2B-AS1,IFT74,LINGO2,PAX5,POLR1E	0.0489359	380	279.65	1.04342
+chr9	65468178	141152931	LOC642236,PGM5,FAM189A2,TRPM3,PRUNE2,GNAQ,NTRK2,ROR2,WNK2,C9orf3,PTCH1,HSD17B3,COL27A1,TNC,ASTN2,DAB2IP,STRBP,NR6A1,PPP6C,CDK9,ABL1,TSC1,SARDH,OLFM1,GPSM1,NOTCH1,MAN1B1	0.0185149	797	596.14	1.02064
+chr10	60500	39076015	ADARB2,IL15RA,UPF2,BEND7,PTER,KIAA1217,GPR158,MPP7,SVIL,PARD3	-0.431773	276	210.322	0.747434
+chr10	42602609	135524247	LOC441666,RET,A1CF,PRKG1,IPMK,M1,CTNNA3,CCAR1,CDH23,FAM149B1,C10orf11,ZMIZ1,NRG3,PTEN,KIF20B,PCGF5,TNKS2,PLCE1,CYP2C8,ENTPD1,HPSE2,CWF19L1,SUFU,SORCS3,RBM20,SHOC2,ATRNL1,INPP5F,FGFR2,UROS,DOCK1,KNDC1	-0.451548	802	606.962	0.736925
+chr11	60500	51566742	HRAS,MOB2,NAP1L4,OLFML1,NRIP3,PTH,SERGEF,NAV2,NELL1,IMMP1L,WT1,QSER1,ELF5,LDLRAD3,LRRC4C,TTC17,AMBRA1,PTPRJ	0.0196477	380	287.827	1.01989
+chr11	55028438	134946016	FADS1,SF1,MEN1,YIF1A,GSTP1,ALDH3B1,CCND1,SHANK2,CLPB,MRPL48,TSKU,GAB2,DLG2,SYTL2,GRM5,MRE11A,AMOTL1,MAML2,YAP1,GUCY1A2,ACAT1,ATM,ZBTB16,MLL,CBL,TRIM29,SORL1,CLMP,SIAE,CHEK1,NTM	-0.00117398	816	614.453	1.00497
+chr12	60500	11993912	ERC1,TULP3,CCND2,ANO2,CD163L1,A2ML1,ETV6	0.0307168	122	92.3914	1.02728
+chr12	11993911	12273512	ETV6	-0.185659	93	71.6682	0.882144
+chr12	12274011	34431528	LRP6,CDKN1B,MGST1,PLEKHA5,SOX5,KRAS,CCDC91,PKP2	-0.0185943	198	147.425	0.994463
+chr12	37857193	41701437	-	-0.409211	25	18.5549	0.760009
+chr12	41701436	42901265	-	2.77937	9	6.926	7.00501
+chr12	42901264	57607768	NELL2,ARID2,TUBA1B,DIP2B,ATF1,ATF7,ERBB3,BAZ2A	-0.479329	181	135.552	0.721699
+chr12	57607767	57914222	DDIT3	3.05428	10	6.95964	8.37521
+chr12	57914721	58520144	CDK4	3.53273	12	8.57114	11.5983
+chr12	58520643	60916332	SLC16A7	3.07097	17	12.9918	8.43946
+chr12	60916331	66908608	SRGAP1	-0.432304	43	33.0768	0.745831
+chr12	66908607	67954874	-	-0.0579432	8	6.26063	0.966245
+chr12	67954873	69003947	-	2.10195	8	6.11156	4.34939
+chr12	69004446	69669616	MDM2	2.817	17	12.3802	7.06433
+chr12	69669615	70541066	-	2.34943	7	5.12415	5.10572
+chr12	70541565	85204790	SYT1,PTPRQ	-0.444059	106	82.5938	0.747667
+chr12	85204789	88658400	LRRIQ1,CEP290	0.0166753	25	19.4678	1.01696
+chr12	88658399	92702070	DUSP6,ATP2B1,LUM	-0.224644	47	35.044	0.862747
+chr12	92702069	133841395	UHRF1BP1L,MYBPC1,CHST11,NUAK1,BTBD11,USP30,PPTC7,NAA25,PTPN11,MAP1LC3B2,HNF1A,RSRC2,ZNF664-FAM101A,TMEM132C,ZNF605	0.0261092	328	251.346	1.02341
+chr13	19020500	105152288	ANKRD26P3,CRYL1,CDK8,FLT3,FLT1,TEX26-AS1,BRCA2,N4BP2L2,RFC3,NBEA,ALG5,EPSTI1,RB1,PCDH9,KLHL1,EDNRB,SPRY2,GPC6,ABCC4,FARP1,CLYBL	0.0119441	804	604.201	1.01461
+chr13	105152287	107418370	-	-0.45566	16	12.5671	0.734405
+chr13	107418369	110108034	FAM155A,MYO16	0.0555301	20	15.5177	1.05008
+chr13	110108033	111460835	IRS2,COL4A2	-0.417517	26	18.2627	0.755855
+chr13	111460834	112353494	-	0.672955	6	4.71689	1.61703
+chr13	112510572	115109378	GRTP1	-0.393884	17	13.2874	0.770523
+chr14	19057400	20346012	-	0.497337	13	7.21662	1.44168
+chr14	20346511	107289040	BCL2L2,THTPA,STXBP6,NOVA1,MIR548AI,AP4S1,AKAP6,RALGAPA1,NKX2-1,SLC25A21,MDGA2,SOS2,ATL1,NID2,SOCS4,C14orf37,CCDC175,SLC38A6,SYNE2,ESR2,FUT8,GPHN,MAP3K9,SIPA1L1,LTBP2,IFT43,SPTLC2,NRXN3,CEP128,TSHR,FOXN3,RPS6KA5,DDX24,GLRX5,HSP90AA1,KLC1,AKT1	0.020917	735	556.033	1.02182
+chr15	20044632	21398319	NBEAP1	-0.266834	13	6.96087	0.837944
+chr15	22262613	66511021	LOC727924,HERC2,TJP1,TRPM1,ATPBD4-AS1,SPRED1,FSIP1,PAK6,LTK,MGA,EPB42,SEMA6D,GALK2,SPPL2A,MYO5C,WDR72,RAB27A,ZNF280D,RORA,TLN2,CSNK1G1	-0.456207	432	321.136	0.735504
+chr15	66511020	102520892	MAP2K1,SMAD3,AAGAB,ANP32A,THSD4,NEO1,LOC729911,BCL2A1,FAM108C1,EFTUD1,AGBL1,NTRK3,RHCG,IDH2,PRC1,C15orf32,LOC145820,FAM169B,IGF1R,ADAMTS17,PCSK6	0.351641	645	498.162	1.2814
+chr16	60500	35148746	CLCN7,TSC2,PDPK1,KREMEN2,CREBBP,DNAJA3,RBFOX1,USP7,GRIN2A,ATF7IP2,SOCS1,PDXDC1,TMC5,DNAH3,PALB2,SULT1A1,BOLA2B,INO80E,ZNF668,FUS	0.0382109	429	312.9	1.03599
+chr16	46457167	63157986	ANKRD26P1,CYLD,TOX3,FTO,NLRC5,NDRG4	-0.432499	151	113.232	0.745492
+chr16	63157985	90294253	CDH5,CDH1,TMCO7,NQO1,PHLPP2,PKD1L3,WDR59,CNTNAP4,VAT1L,NECAB2,ZNF276,DEF8	0.0574363	266	202.965	1.04681
+chr17	500	22220573	WSCD1,FXR2,TP53,AURKB,NTN1,MAP2K4,HS3ST3A1,DRG2	0.0412136	194	143.626	1.03551
+chr17	25268558	27481069	-	0.0638443	19	13.4016	1.05191
+chr17	27481068	30711280	NSRP1,NF1,RHOT1	-0.474127	112	79.2826	0.723406
+chr17	30711279	81194710	ASIC2,ZNHIT3,DDX52,FBXL20,ERBB2,RARA,STAT3,BRCA1,DCAKD,CRHR1,GOSR2,SKAP1,COL1A1,PPM1E,BRIP1,TANC2,CD79B,PRKCA,MAP2K6,LINC00673,CASKIN2,DNAH17,RPTOR,NPLOC4	0.0132405	585	430.786	1.01651
+chr18	10500	15381134	C18orf56,TYMS,LPIN2,L3MBTL4,C18orf1	0.0163384	111	82.753	1.01884
+chr18	18520841	78016748	ROCK1,CDH2,FAM59A,NOL4,INO80C,KIAA1328,RIT2,EPG5,SMAD2,DYM,SMAD4,DCC,RAB27B,TCF4,LMAN1,CDH20,TNFRSF11A,BCL2,DOK6,NETO1,PARD6G	0.0277852	552	414.695	1.02524
+chr19	60500	24364012	STK11,DOT1L,TLE2,GNA11,GIPC3,MAP2K2,LOC100128568,INSR,ARHGEF18,MUC16,CDC37,KEAP1,SMARCA4,CACNA1A,PODNL1,NOTCH3,EPS15L1,JAK3,SLC5A5,GATAD2A,RPSAP58	0.0590614	380	273.512	1.05042
+chr19	28263181	59118483	LOC284395,CCNE1,CEBPA,RYR1,ZNF546,AKT2,LOC100505495,CD79A,GSK3A,PSG11,CEACAM20,ERCC2,CCDC61,BCL2L12,LRRC4B,ZNF615,LOC100128252,ZNF606	0.0648454	295	218.048	1.05252
+chr20	60500	26256532	SIRPD,PTPRA,ITPA,CRLS1,PLCB4,C20orf94,MACROD2,KIF16B,OVOL2,SLC24A3,NINL	-0.00373834	192	148.644	1.00306
+chr20	29420068	62965020	DEFB116,ITCH,SRC,PPP1R16B,TOP1,PLCG1,YWHAB,ELMO2,AURKA,VAPB,GNAS-AS1,GNAS,CDH4,ARFRP1	0.00881644	353	260.977	1.01394
+chr21	9411693	11185554	-	0.167098	11	5.57339	1.14139
+chr21	14370290	25345441	LIPI,RBM11,CHODL,NCAM2	-0.0172463	87	64.9672	0.994992
+chr21	25345440	48119395	RUNX1,CBR3-AS1,KCNJ6,ERG,DSCAM,UMODL1,HSF2BP,SLC19A1	-0.370098	193	145.608	0.779093
+chr22	16050500	25501410	TPTEP1,ANKRD62P1-PARP4P3,XKR3,CECR2,CLDN5,CRKL,GUSBP11,SMARCB1,KIAA1671	0.0851634	95	66.3061	1.07015
+chr22	25501909	30061095	CRYBB1,TTC28,CHEK2,EWSR1,NF2	-0.0626938	115	85.8246	0.96186
+chr22	30064267	39483505	NF2,SYN3,MB,RAC2,SOX10,APOBEC3G	0.0527237	95	72.038	1.04177
+chr22	39484004	39637713	PDGFB	-0.335444	23	17.4422	0.794597
+chr22	39637712	42059851	PDGFB,TNRC6B,EP300,DESI1,XRCC6	-0.0435486	89	65.3698	0.976478
+chr22	42060350	51244066	CYP2D6,BIK,LINC00229,FLJ46257,CPT1B	0.0899123	74	56.0008	1.06929
+chrX	60500	2561647	CRLF2	1.52253	23	12.4313	2.97132
+chrX	2561646	4653265	XG,ARSF	2.32422	17	12.2041	5.13739
+chrX	4653264	10942673	NLGN4X	0.951266	45	34.0583	2.14257
+chrX	10942672	13652870	-	2.40566	20	15.1003	5.34066
+chrX	13652869	16352969	-	0.917729	19	13.9893	1.89738
+chrX	16352968	19499971	-	2.45883	23	17.4682	5.66689
+chrX	19501149	23404334	LOC100873065	2.80571	27	21.338	7.02158
+chrX	23404333	31504390	KLHL15,DMD	1.15411	60	46.0369	2.34853
+chrX	31504889	34071142	DMD	2.55621	17	13.0783	5.99214
+chrX	34071141	40507998	LANCL3	0.924811	46	36.1274	1.90599
+chrX	40508497	47864357	USP9X,KDM6A,CXorf36,SLC9A7,ARAF	2.11837	155	110.869	4.38767
+chrX	47864356	55358602	GATA1,PHF8	1.30972	59	41.6211	2.49803
+chrX	55358601	58180101	SPIN3	0.898777	21	15.3586	1.87247
+chrX	61931663	80426930	ARHGEF9,AR,OPHN1,EDA,BCYRN1,PIN4,FTX,TBX22	0.910314	177	131.052	1.89139
+chrX	80426929	94676963	DACH2,PCDH11X	0.772685	101	73.4768	1.72826
+chrX	94676962	155260060	DIAPH2,LOC442459,BHLHB9,IL1RAPL2,AMMECR1,PAK3,ALG13,HTR2C,XIAP,STAG2,HS6ST2,FMR1-AS1,CD99L2,GABRA3,FAM58A	0.92881	488	360.256	1.92276
+chrY	10500	2654042	-	1.43559	17	11.0704	2.86884
+chrY	2654541	28649168	-	-3.72105	144	98.5636	0.130802
+chrY	59099791	59363066	-	-0.0244204	2	1.48068	0.989748