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consts.py
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consts.py
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#CNPriors=[1.6e-3,4e-3,0.98,1e-2,1e-4,1e-6,1e-8,1e-10,1e-12,1e-14,1e-16]
#CNPriors=[7.417780287723428e-08, 0.0005430425794006451, 0.9938810356257187, 0.004973460814692634, 0.0005568941112454805, 3.311346957020157e-05, 9.880601377129313e-06, 1.7439974793564956e-06, 5.833123605834217e-07, 7.081061413515137e-08, 1.0017795735509531e-07]
#calculated by python3 statcnf.py ~/data/1000gp/*genotypes.vcf.gz, using 1000gp phase3 vcf
#CNPriors=[7.728128828742843e-08, 0.0005542635683200515, 0.9937998585099401, 0.004991815235125496, 0.0005993279221639579, 4.027205707560094e-05, 1.1303333014597475e-05, 2.324967195279671e-06, 5.85496445434659e-07, 7.108336483016042e-08, 1.0021139153473964e-07]
#CNPriors=[1.4818669642343562e-06, 0.0024241621501567266, 0.9914186177260093, 0.00550095102642564, 0.0006000125666241987, 4.0389660750366106e-05, 1.1302181811873978e-05, 2.3256457943417974e-06, 5.854614618138028e-07, 7.124415377290356e-08, 1.0010930675953374e-07, 3.210044872566197e-10, 3.565148390433508e-11, 2.993635914964604e-12, 7.20618688429682e-13, 1.3465236956844422e-13, 3.0109007332307176e-14, 3.4497272100312798e-15, 2.5051103812841497e-15, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
CNPriors=[1.4818669642343562e-06, 0.0024241621501567266, 0.9914186177260093, 0.00550095102642564, 0.0006000125666241987, 4.0389660750366106e-05, 1.1302181811873978e-05, 2.3256457943417974e-06, 5.854614618138028e-07, 7.124415377290356e-08, 1.0010930675953374e-07, 3.210044872566197e-10, 3.565148390433508e-11, 2.993635914964604e-12, 7.20618688429682e-13, 1.3465236956844422e-13, 3.0109007332307176e-14, 3.4497272100312798e-15, 2.5051103812841497e-15]
DefaultHeader="""##fileformat=VCFv4.1
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate=20150218
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##contig=<ID=Y,assembly=b37,length=59373566>
##contig=<ID=hs37d5,assembly=b37,length=35477943>
##ALT=<ID=CNV,Description="Copy Number Polymorphism">
##ALT=<ID=DEL,Description="Deletion">
##ALT=<ID=DUP,Description="Duplication">
##ALT=<ID=INS:ME:ALU,Description="Insertion of ALU element">
##ALT=<ID=INS:ME:LINE1,Description="Insertion of LINE1 element">
##ALT=<ID=INS:ME:SVA,Description="Insertion of SVA element">
##ALT=<ID=INS:MT,Description="Nuclear Mitochondrial Insertion">
##ALT=<ID=INV,Description="Inversion">
##ALT=<ID=CN0,Description="Copy number allele: 0 copies">
##ALT=<ID=CN1,Description="Copy number allele: 1 copy">
##ALT=<ID=CN2,Description="Copy number allele: 2 copies">
##ALT=<ID=CN3,Description="Copy number allele: 3 copies">
##ALT=<ID=CN4,Description="Copy number allele: 4 copies">
##ALT=<ID=CN5,Description="Copy number allele: 5 copies">
##ALT=<ID=CN6,Description="Copy number allele: 6 copies">
##ALT=<ID=CN7,Description="Copy number allele: 7 copies">
##ALT=<ID=CN8,Description="Copy number allele: 8 copies">
##ALT=<ID=CN9,Description="Copy number allele: 9 copies">
##ALT=<ID=CN10,Description="Copy number allele: 10 copies">
##ALT=<ID=CN11,Description="Copy number allele: 11 copies">
##ALT=<ID=CN12,Description="Copy number allele: 12 copies">
##ALT=<ID=CN13,Description="Copy number allele: 13 copies">
##ALT=<ID=CN14,Description="Copy number allele: 14 copies">
##ALT=<ID=CN15,Description="Copy number allele: 15 copies">
##ALT=<ID=CN16,Description="Copy number allele: 16 copies">
##ALT=<ID=CN17,Description="Copy number allele: 17 copies">
##ALT=<ID=CN18,Description="Copy number allele: 18 copies">
##ALT=<ID=CN19,Description="Copy number allele: 19 copies">
##ALT=<ID=CN20,Description="Copy number allele: 20 copies">
##ALT=<ID=CN21,Description="Copy number allele: 21 copies">
##ALT=<ID=CN22,Description="Copy number allele: 22 copies">
##ALT=<ID=CN23,Description="Copy number allele: 23 copies">
##ALT=<ID=CN24,Description="Copy number allele: 24 copies">
##ALT=<ID=CN25,Description="Copy number allele: 25 copies">
##ALT=<ID=CN26,Description="Copy number allele: 26 copies">
##ALT=<ID=CN27,Description="Copy number allele: 27 copies">
##ALT=<ID=CN28,Description="Copy number allele: 28 copies">
##ALT=<ID=CN29,Description="Copy number allele: 29 copies">
##ALT=<ID=CN30,Description="Copy number allele: 30 copies">
##ALT=<ID=CN31,Description="Copy number allele: 31 copies">
##ALT=<ID=CN32,Description="Copy number allele: 32 copies">
##ALT=<ID=CN33,Description="Copy number allele: 33 copies">
##ALT=<ID=CN34,Description="Copy number allele: 34 copies">
##ALT=<ID=CN35,Description="Copy number allele: 35 copies">
##ALT=<ID=CN36,Description="Copy number allele: 36 copies">
##ALT=<ID=CN37,Description="Copy number allele: 37 copies">
##ALT=<ID=CN38,Description="Copy number allele: 38 copies">
##ALT=<ID=CN39,Description="Copy number allele: 39 copies">
##ALT=<ID=CN40,Description="Copy number allele: 40 copies">
##ALT=<ID=CN41,Description="Copy number allele: 41 copies">
##ALT=<ID=CN42,Description="Copy number allele: 42 copies">
##ALT=<ID=CN43,Description="Copy number allele: 43 copies">
##ALT=<ID=CN44,Description="Copy number allele: 44 copies">
##ALT=<ID=CN45,Description="Copy number allele: 45 copies">
##ALT=<ID=CN46,Description="Copy number allele: 46 copies">
##ALT=<ID=CN47,Description="Copy number allele: 47 copies">
##ALT=<ID=CN48,Description="Copy number allele: 48 copies">
##ALT=<ID=CN49,Description="Copy number allele: 49 copies">
##ALT=<ID=CN50,Description="Copy number allele: 50 copies">
##ALT=<ID=CN51,Description="Copy number allele: 51 copies">
##ALT=<ID=CN52,Description="Copy number allele: 52 copies">
##ALT=<ID=CN53,Description="Copy number allele: 53 copies">
##ALT=<ID=CN54,Description="Copy number allele: 54 copies">
##ALT=<ID=CN55,Description="Copy number allele: 55 copies">
##ALT=<ID=CN56,Description="Copy number allele: 56 copies">
##ALT=<ID=CN57,Description="Copy number allele: 57 copies">
##ALT=<ID=CN58,Description="Copy number allele: 58 copies">
##ALT=<ID=CN59,Description="Copy number allele: 59 copies">
##ALT=<ID=CN60,Description="Copy number allele: 60 copies">
##ALT=<ID=CN61,Description="Copy number allele: 61 copies">
##ALT=<ID=CN62,Description="Copy number allele: 62 copies">
##ALT=<ID=CN63,Description="Copy number allele: 63 copies">
##ALT=<ID=CN64,Description="Copy number allele: 64 copies">
##ALT=<ID=CN65,Description="Copy number allele: 65 copies">
##ALT=<ID=CN66,Description="Copy number allele: 66 copies">
##ALT=<ID=CN67,Description="Copy number allele: 67 copies">
##ALT=<ID=CN68,Description="Copy number allele: 68 copies">
##ALT=<ID=CN69,Description="Copy number allele: 69 copies">
##ALT=<ID=CN70,Description="Copy number allele: 70 copies">
##ALT=<ID=CN71,Description="Copy number allele: 71 copies">
##ALT=<ID=CN72,Description="Copy number allele: 72 copies">
##ALT=<ID=CN73,Description="Copy number allele: 73 copies">
##ALT=<ID=CN74,Description="Copy number allele: 74 copies">
##ALT=<ID=CN75,Description="Copy number allele: 75 copies">
##ALT=<ID=CN76,Description="Copy number allele: 76 copies">
##ALT=<ID=CN77,Description="Copy number allele: 77 copies">
##ALT=<ID=CN78,Description="Copy number allele: 78 copies">
##ALT=<ID=CN79,Description="Copy number allele: 79 copies">
##ALT=<ID=CN80,Description="Copy number allele: 80 copies">
##ALT=<ID=CN81,Description="Copy number allele: 81 copies">
##ALT=<ID=CN82,Description="Copy number allele: 82 copies">
##ALT=<ID=CN83,Description="Copy number allele: 83 copies">
##ALT=<ID=CN84,Description="Copy number allele: 84 copies">
##ALT=<ID=CN85,Description="Copy number allele: 85 copies">
##ALT=<ID=CN86,Description="Copy number allele: 86 copies">
##ALT=<ID=CN87,Description="Copy number allele: 87 copies">
##ALT=<ID=CN88,Description="Copy number allele: 88 copies">
##ALT=<ID=CN89,Description="Copy number allele: 89 copies">
##ALT=<ID=CN90,Description="Copy number allele: 90 copies">
##ALT=<ID=CN91,Description="Copy number allele: 91 copies">
##ALT=<ID=CN92,Description="Copy number allele: 92 copies">
##ALT=<ID=CN93,Description="Copy number allele: 93 copies">
##ALT=<ID=CN94,Description="Copy number allele: 94 copies">
##ALT=<ID=CN95,Description="Copy number allele: 95 copies">
##ALT=<ID=CN96,Description="Copy number allele: 96 copies">
##ALT=<ID=CN97,Description="Copy number allele: 97 copies">
##ALT=<ID=CN98,Description="Copy number allele: 98 copies">
##ALT=<ID=CN99,Description="Copy number allele: 99 copies">
##ALT=<ID=CN100,Description="Copy number allele: 100 copies">
##ALT=<ID=CN101,Description="Copy number allele: 101 copies">
##ALT=<ID=CN102,Description="Copy number allele: 102 copies">
##ALT=<ID=CN103,Description="Copy number allele: 103 copies">
##ALT=<ID=CN104,Description="Copy number allele: 104 copies">
##ALT=<ID=CN105,Description="Copy number allele: 105 copies">
##ALT=<ID=CN106,Description="Copy number allele: 106 copies">
##ALT=<ID=CN107,Description="Copy number allele: 107 copies">
##ALT=<ID=CN108,Description="Copy number allele: 108 copies">
##ALT=<ID=CN109,Description="Copy number allele: 109 copies">
##ALT=<ID=CN110,Description="Copy number allele: 110 copies">
##ALT=<ID=CN111,Description="Copy number allele: 111 copies">
##ALT=<ID=CN112,Description="Copy number allele: 112 copies">
##ALT=<ID=CN113,Description="Copy number allele: 113 copies">
##ALT=<ID=CN114,Description="Copy number allele: 114 copies">
##ALT=<ID=CN115,Description="Copy number allele: 115 copies">
##ALT=<ID=CN116,Description="Copy number allele: 116 copies">
##ALT=<ID=CN117,Description="Copy number allele: 117 copies">
##ALT=<ID=CN118,Description="Copy number allele: 118 copies">
##ALT=<ID=CN119,Description="Copy number allele: 119 copies">
##ALT=<ID=CN120,Description="Copy number allele: 120 copies">
##ALT=<ID=CN121,Description="Copy number allele: 121 copies">
##ALT=<ID=CN122,Description="Copy number allele: 122 copies">
##ALT=<ID=CN123,Description="Copy number allele: 123 copies">
##ALT=<ID=CN124,Description="Copy number allele: 124 copies">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
##INFO=<ID=CS,Number=1,Type=String,Description="Source call set.">
##INFO=<ID=END,Number=1,Type=Integer,Description="End coordinate of this variant">
##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
##INFO=<ID=MC,Number=.,Type=String,Description="Merged calls.">
##INFO=<ID=MEINFO,Number=4,Type=String,Description="Mobile element info of the form NAME,START,END<POLARITY; If there is only 5' OR 3' support for this call, will be NULL NULL for START and END">
##INFO=<ID=MEND,Number=1,Type=Integer,Description="Mitochondrial end coordinate of inserted sequence">
##INFO=<ID=MLEN,Number=1,Type=Integer,Description="Estimated length of mitochondrial insert">
##INFO=<ID=MSTART,Number=1,Type=Integer,Description="Mitochondrial start coordinate of inserted sequence">
##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="SV length. It is only calculated for structural variation MEIs. For other types of SVs; one may calculate the SV length by INFO:END-START+1, or by finding the difference between lengthes of REF and ALT alleles">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##INFO=<ID=TSD,Number=1,Type=String,Description="Precise Target Site Duplication for bases, if unknown, value will be NULL">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes">
##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1)">
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=EAS_AF,Number=A,Type=Float,Description="Allele frequency in the EAS populations calculated from AC and AN, in the range (0,1)">
##INFO=<ID=EUR_AF,Number=A,Type=Float,Description="Allele frequency in the EUR populations calculated from AC and AN, in the range (0,1)">
##INFO=<ID=AFR_AF,Number=A,Type=Float,Description="Allele frequency in the AFR populations calculated from AC and AN, in the range (0,1)">
##INFO=<ID=AMR_AF,Number=A,Type=Float,Description="Allele frequency in the AMR populations calculated from AC and AN, in the range (0,1)">
##INFO=<ID=SAS_AF,Number=A,Type=Float,Description="Allele frequency in the SAS populations calculated from AC and AN, in the range (0,1)">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth; only low coverage data were counted towards the DP, exome data were not used">
##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele. Format: AA|REF|ALT|IndelType. AA: Ancestral allele, REF:Reference Allele, ALT:Alternate Allele, IndelType:Type of Indel (REF, ALT and IndelType are only defined for indels)">
##INFO=<ID=VT,Number=.,Type=String,Description="indicates what type of variant the line represents">
##INFO=<ID=EX_TARGET,Number=0,Type=Flag,Description="indicates whether a variant is within the exon pull down target boundaries">
##INFO=<ID=MULTI_ALLELIC,Number=0,Type=Flag,Description="indicates whether a site is multi-allelic">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT"""