- or download this
#!/usr/bin/perl;
use strict; use v5.8.8;
use Data::Dumper;
...
}
close OUT;
- or download this
--Dummydata1.var--
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT
+ IFS003-W Chr Start End Ref Alt Func.refGene G
+ene.refGene GeneDetail.refGene ExonicFunc.refGene AAChange.r
+efGene Func.knownGene Gene.knownGene GeneDetail.knownGene
+ ExonicFunc.knownGene AAChange.knownGene avsnp144 1000g2015a
+ug_all 1000g2015aug_afr 1000g2015aug_amr 1000g2015aug_sas
+ 1000g2015aug_eur 1000g2015aug_eas esp6500siv2_all esp6500si
+v2_ea esp6500siv2_aa ExAC_ALL ExAC_AFR ExAC_AMR ExAC_E
+AS ExAC_FIN ExAC_NFE ExAC_OTH ExAC_SAS cosmic70 SIF
+T_score SIFT_pred Polyphen2_HDIV_score Polyphen2_HDIV_pred
+ Polyphen2_HVAR_score Polyphen2_HVAR_pred LRT_score LRT_pre
+d MutationTaster_score MutationTaster_pred MutationAssessor_
+score MutationAssessor_pred FATHMM_score FATHMM_pred PROV
+EAN_score PROVEAN_pred VEST3_score CADD_raw CADD_phred
+ DANN_score fathmm-MKL_coding_score fathmm-MKL_coding_pred M
+etaSVM_score MetaSVM_pred MetaLR_score MetaLR_pred integr
+ated_fitCons_score integrated_confidence_value GERP++_RS phy
+loP7way_vertebrate phyloP20way_mammalian phastCons7way_vertebra
+te phastCons20way_mammalian SiPhy_29way_logOdds Interpro_dom
+ain dbscSNV_ADA_SCORE dbscSNV_RF_SCORE CLINSIG CLNDBN
+CLNACC CLNDSDB CLNDSDBID HRC_AF HRC_AC HRC_AN HRC_n
+on1000G_AF HRC_non1000G_AC HRC_non1000G_AN Kaviar_AF Kavi
+ar_AC Kaviar_AN nci60 KEY3 INFO_AC INFO_AF INFO_Bas
+eQRankSum INFO_ClippingRankSum INFO_DP INFO_DS INFO_END
+ INFO_ExcessHet INFO_FS INFO_HaplotypeScore INFO_Inbreeding
+Coeff INFO_MLEAC INFO_MLEAF INFO_MQ INFO_MQRankSum INF
+O_QD INFO_RAW_MQ INFO_ReadPosRankSum INFO_SOR seq seq_
+flag AAchange Grantham Mutability FuentesFalsePositive
+ ACMG
chr1 14653 . C T 191.77 . AC=1;AF=0.500;AN=2;Base
+QRankSum=1.23;ClippingRankSum=0.00;DP=26;ExcessHet=3.0103;FS=6.641;ML
+EAC=1;MLEAF=0.500;MQ=32.19;MQRankSum=0.580;QD=7.38;ReadPosRankSum=-1.
+830e-01;SOR=2.280 GT:AD:DP:GQ:PL 0/1:15,11:26:99:220,0,292 c
+hr1 14653 14653 C T ncRNA_exonic WASH7P
+ intergenic NONE,MIR6859-3 dist=NONE;dist=2716 rs
+62635297
+
+
+
+0.0011526 30 26028 chr1:14653:14653:C:T 1 0.5 1
+.23 0 26 no_DS no_END 3.0103 6.641 no_HaplotypeS
+core no_InbreedingCoeff 1 0.5 32.19 0.58 7.38 no
+_RAW_MQ -1.83E-01 2.28 AAGGAAGTAGGTCTGAGCAGCTTGTCCTGGCTGTGTC
+CATGTCAGAGCAA[C]GGCCCAAGTCTGGGTCTGGGGGGGAAGGTGTCATGGAGCCCCCTACGATT
+ pass XX . 0 1 0
...
chr1 17385 . G A 81.77 . AC=1;AF=0.500;AN=2;BaseQ
+RankSum=0.653;ClippingRankSum=0.00;DP=71;ExcessHet=3.0103;FS=3.091;ML
+EAC=1;MLEAF=0.500;MQ=48.65;MQRankSum=0.417;QD=1.15;ReadPosRankSum=1.0
+2;SOR=0.311 GT:AD:DP:GQ:PL 0/1:60,11:71:99:110,0,1715 chr1
+ 17385 17385 G A ncRNA_exonic;splicing MIR6859-1,MIR6
+859-2,MIR6859-3,MIR6859-4;WASH7P NR_024540:exon6:c.588-17C>T
+ ncRNA_exonic MIR6859-3 rs201535981
+ 0.2454 0.2331 0.2857 0.0423
+0.2817 0.2743 0.2321 0.2092
+
+
+ 0.0015912 246 154602 chr1:1
+7385:17385:G:A 1 0.5 0.653 0 71 no_DS no_END
+3.0103 3.091 no_HaplotypeScore no_InbreedingCoeff 1 0.
+5 48.65 0.417 1.15 no_RAW_MQ 1.02 0.311 AGCCAGGG
+GGTCCAGGAAGACATACTTCTTCTACCTACAGAGGCGACATG[G]GGGTCAGGCAAGCTGACACCCGCT
+GTCCTGAGCCCATGTTCCTCTCCCAC pass XX . 0 0 0
chr1 17408 . C G 134.77 . AC=1;AF=0.500;AN=2;Base
+QRankSum=-9.480e-01;ClippingRankSum=0.00;DP=94;ExcessHet=3.0103;FS=0.
+000;MLEAC=1;MLEAF=0.500;MQ=52.27;MQRankSum=-8.570e-01;QD=1.45;ReadPos
+RankSum=0.359;SOR=0.527 GT:AD:DP:GQ:PL 0/1:79,14:93:99:163,0,23
+39 chr1 17408 17408 C G ncRNA_exonic MIR6859-1,M
+IR6859-2,MIR6859-3,MIR6859-4 ncRNA_exonic MIR6859-3
+ rs747093451 0.
+0352 0.0339 0.049 0 0.0273 0.0438 0 0.0074
+
+
+ 0.0013842
+214 154602 chr1:17408:17408:C:G 1 0.5 -9.48E-01
+ 0 94 no_DS no_END 3.0103 0 no_HaplotypeScore no
+_InbreedingCoeff 1 0.5 52.27 -8.57E-01 1.45 no_RAW_
+MQ 0.359 0.527 ACTTCTTCTACCTACAGAGGCGACATGGGGGTCAGGCAAGCTGAC
+ACCCG[C]TGTCCTGAGCCCATGTTCCTCTCCCACATCATCAGGGGCACAGCGTGCAC pass
+ XX . 0 0 0
chr1 17697 . G C 125.77 . AC=1;AF=0.500;AN=2;Base
+QRankSum=-2.529e+00;ClippingRankSum=0.00;DP=28;ExcessHet=3.0103;FS=0.
+000;MLEAC=1;MLEAF=0.500;MQ=39.25;MQRankSum=-8.310e-01;QD=4.49;ReadPos
+RankSum=1.07;SOR=0.124 GT:AD:DP:GQ:PL 0/1:21,7:28:99:154,0,714
+ chr1 17697 17697 G C ncRNA_exonic WASH7P
+ upstream MIR6859-3 rs374995955
+
+
+
+ 0.0155602 405 2
+6028 chr1:17697:17697:G:C 1 0.5 -2.53E+00 0 28
+ no_DS no_END 3.0103 0 no_HaplotypeScore no_Inbreedi
+ngCoeff 1 0.5 39.25 -8.31E-01 4.49 no_RAW_MQ 1.0
+7 0.124 GCTGATGTTGCTGGGAAGACCCCCAAGTCCCTCTTCTGCATCGTCCTCGG[G]CT
+CCGGCTTGGTGCTCACGCACACAGGAAAGTCCTTCAGCTTCTCCTGAG pass XX .
+ 0 1 0
- or download this
--Dummydata2.var--
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT
+ IFS001_W1515808 Chr Start End Ref Alt Func.refGe
+ne Gene.refGene GeneDetail.refGene ExonicFunc.refGene AAC
+hange.refGene Func.knownGene Gene.knownGene GeneDetail.known
+Gene ExonicFunc.knownGene AAChange.knownGene avsnp144 100
+0g2015aug_all 1000g2015aug_afr 1000g2015aug_amr 1000g2015aug
+_sas 1000g2015aug_eur 1000g2015aug_eas esp6500siv2_all es
+p6500siv2_ea esp6500siv2_aa ExAC_ALL ExAC_AFR ExAC_AMR
+ ExAC_EAS ExAC_FIN ExAC_NFE ExAC_OTH ExAC_SAS cosmic70
+ SIFT_score SIFT_pred Polyphen2_HDIV_score Polyphen2_HDIV
+_pred Polyphen2_HVAR_score Polyphen2_HVAR_pred LRT_score
+LRT_pred MutationTaster_score MutationTaster_pred MutationAs
+sessor_score MutationAssessor_pred FATHMM_score FATHMM_pred
+ PROVEAN_score PROVEAN_pred VEST3_score CADD_raw CADD_p
+hred DANN_score fathmm-MKL_coding_score fathmm-MKL_coding_pr
+ed MetaSVM_score MetaSVM_pred MetaLR_score MetaLR_pred
+ integrated_fitCons_score integrated_confidence_value GERP++_RS
+ phyloP7way_vertebrate phyloP20way_mammalian phastCons7way_v
+ertebrate phastCons20way_mammalian SiPhy_29way_logOdds Inter
+pro_domain dbscSNV_ADA_SCORE dbscSNV_RF_SCORE CLINSIG CLN
+DBN CLNACC CLNDSDB CLNDSDBID HRC_AF HRC_AC HRC_AN
+ HRC_non1000G_AF HRC_non1000G_AC HRC_non1000G_AN Kaviar_AF
+ Kaviar_AC Kaviar_AN nci60 KEY3 INFO_AC INFO_AF I
+NFO_BaseQRankSum INFO_ClippingRankSum INFO_DP INFO_DS INF
+O_END INFO_ExcessHet INFO_FS INFO_HaplotypeScore INFO_Inb
+reedingCoeff INFO_MLEAC INFO_MLEAF INFO_MQ INFO_MQRankSum
+ INFO_QD INFO_RAW_MQ INFO_ReadPosRankSum INFO_SOR seq
+ seq_flag AAchange Grantham Mutability FuentesFalsePosi
+tive ACMG
chr1 14464 . A T 39.77 . AC=1;AF=0.500;AN=2;BaseQ
+RankSum=1.38;ClippingRankSum=0.00;DP=4;ExcessHet=3.0103;FS=0.000;MLEA
+C=1;MLEAF=0.500;MQ=40.51;MQRankSum=-6.740e-01;QD=9.94;ReadPosRankSum=
+0.674;SOR=2.303 GT:AD:DP:GQ:PL 0/1:2,2:4:64:68,0,64 chr1
+14464 14464 A T ncRNA_exonic WASH7P int
+ergenic NONE,MIR6859-3 dist=NONE;dist=2905 rs5461694
+44 0.0958466 0.0144 0.1138 0.1943 0.1859 0.005
+
+
+
+ 0.0346166 901 26028 chr1
+:14464:14464:A:T 1 0.5 1.38 0 4 no_DS no_END
+3.0103 0 no_HaplotypeScore no_InbreedingCoeff 1 0.5
+ 40.51 -6.74E-01 9.94 no_RAW_MQ 0.674 2.303 GTTCTTT
+ATTGATTGGTGTGCCGTTTTCTCTGGAAGCCTCTTAAGAACAC[A]GTGGCGCAGGCTGGGTGGAGCCG
+TCCCCCCATGGAGCACAGGCAGACAGA pass XX . 0 1 0
...
chr1 138156 . G T 120.84 . AC=2;AF=1.00;AN=2;DP=6
+;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=20.17;QD=20.14;SOR=0
+.693 GT:AD:DP:GQ:PL 1/1:0,6:6:18:149,18,0 chr1 138156
+138156 G T ncRNA_exonic LOC729737 intergen
+ic RP11-34P13.7,RP11-34P13.14 dist=4433;dist=1634 rs
+370691115
+
+
+
+ 0.0967804 2519 26028 chr1:138156:138156:G:T 2 1
+ no_BaseQRankSum no_ClippingRankSum 6 no_DS no_END 3.
+0103 0 no_HaplotypeScore no_InbreedingCoeff 2 1 20.
+17 no_MQRankSum 20.14 no_RAW_MQ no_ReadPosRankSum 0.69
+3 GGACTCGGGAGGCCGCAGTGAAGCAACAGCTAGCTGGGCGTGGAGAGTCC[G]CTGTGAGGCAG
+AGGCTGGGCCTGTGCAGGCCTTCGGGAGGCAGGAGGCTG pass XX . 0 0
+ 0
chr1 139213 . A G 1774.77 . AC=1;AF=0.500;AN=2;Ba
+seQRankSum=-4.140e+00;ClippingRankSum=0.00;DP=97;ExcessHet=3.0103;FS=
+3.809;MLEAC=1;MLEAF=0.500;MQ=39.41;MQRankSum=-1.653e+00;QD=18.30;Read
+PosRankSum=-7.760e-01;SOR=1.060 GT:AD:DP:GQ:PGT:PID:PL 0/1:51,4
+6:97:99:0|1:139213_A_G:1803,0,3192 chr1 139213 139213 A
+ G ncRNA_exonic LOC729737 downstream RP11-34
+P13.14 rs370723703
+ 0.2506 0.3787 0.2879 0.3404 0.25 0.2597 0.3083
+ 0.2352
+
+
+ 0.0259699 4015 154602 chr1:139213:139213:A:G 1 0
+.5 -4.14E+00 0 97 no_DS no_END 3.0103 3.809 n
+o_HaplotypeScore no_InbreedingCoeff 1 0.5 39.41 -1.65E
++00 18.3 no_RAW_MQ -7.76E-01 1.06 GGAAGGTTGCCATGAGACAA
+AAGTTGGGCCTGGAAAGGCCCTTGTGAAGC[A]TGAGCTTGGCCTAAAGAGGCCACTGGGTGGCAGGAG
+CTGGGTGTGTAGAA pass XX . 0 0 0
chr1 139233 . C A 1883.77 . AC=1;AF=0.500;AN=2;Ba
+seQRankSum=-9.990e-01;ClippingRankSum=0.00;DP=110;ExcessHet=3.0103;FS
+=2.463;MLEAC=1;MLEAF=0.500;MQ=39.80;MQRankSum=0.636;QD=17.13;ReadPosR
+ankSum=-1.834e+00;SOR=0.595 GT:AD:DP:GQ:PGT:PID:PL 0/1:56,54:11
+0:99:0|1:139213_A_G:1912,0,3261 chr1 139233 139233 C A
+ ncRNA_exonic LOC729737 downstream RP11-34P13
+.14 rs373847457
+ 0.2478 0.3763 0.2985 0.3548 . 0.2577 0.3103 0.2
+308
+
+ 0.02
+54654 3937 154602 chr1:139233:139233:C:A 1 0.5
+-9.99E-01 0 110 no_DS no_END 3.0103 2.463 no_Hap
+lotypeScore no_InbreedingCoeff 1 0.5 39.8 0.636 17.
+13 no_RAW_MQ -1.83E+00 0.595 AAGTTGGGCCTGGAAAGGCCCTTGTGAA
+GCATGAGCTTGGCCTAAAGAGG[C]CACTGGGTGGCAGGAGCTGGGTGTGTAGAAGCTGCTGAAAGGTT
+GGGAGC pass XX . 0 0 0
- or download this
--Dummydata3.var--
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT
+ IFS002_W1600378 Chr Start End Ref Alt Func.refGe
+ne Gene.refGene GeneDetail.refGene ExonicFunc.refGene AAC
+hange.refGene Func.knownGene Gene.knownGene GeneDetail.known
+Gene ExonicFunc.knownGene AAChange.knownGene avsnp144 100
+0g2015aug_all 1000g2015aug_afr 1000g2015aug_amr 1000g2015aug
+_sas 1000g2015aug_eur 1000g2015aug_eas esp6500siv2_all es
+p6500siv2_ea esp6500siv2_aa ExAC_ALL ExAC_AFR ExAC_AMR
+ ExAC_EAS ExAC_FIN ExAC_NFE ExAC_OTH ExAC_SAS cosmic70
+ SIFT_score SIFT_pred Polyphen2_HDIV_score Polyphen2_HDIV
+_pred Polyphen2_HVAR_score Polyphen2_HVAR_pred LRT_score
+LRT_pred MutationTaster_score MutationTaster_pred MutationAs
+sessor_score MutationAssessor_pred FATHMM_score FATHMM_pred
+ PROVEAN_score PROVEAN_pred VEST3_score CADD_raw CADD_p
+hred DANN_score fathmm-MKL_coding_score fathmm-MKL_coding_pr
+ed MetaSVM_score MetaSVM_pred MetaLR_score MetaLR_pred
+ integrated_fitCons_score integrated_confidence_value GERP++_RS
+ phyloP7way_vertebrate phyloP20way_mammalian phastCons7way_v
+ertebrate phastCons20way_mammalian SiPhy_29way_logOdds Inter
+pro_domain dbscSNV_ADA_SCORE dbscSNV_RF_SCORE CLINSIG CLN
+DBN CLNACC CLNDSDB CLNDSDBID HRC_AF HRC_AC HRC_AN
+ HRC_non1000G_AF HRC_non1000G_AC HRC_non1000G_AN Kaviar_AF
+ Kaviar_AC Kaviar_AN nci60 KEY3 INFO_AC INFO_AF I
+NFO_BaseQRankSum INFO_ClippingRankSum INFO_DP INFO_DS INF
+O_END INFO_ExcessHet INFO_FS INFO_HaplotypeScore INFO_Inb
+reedingCoeff INFO_MLEAC INFO_MLEAF INFO_MQ INFO_MQRankSum
+ INFO_QD INFO_RAW_MQ INFO_ReadPosRankSum INFO_SOR seq
+ seq_flag AAchange Grantham Mutability FuentesFalsePosi
+tive ACMG
chr1 14590 . G A 118.77 . AC=1;AF=0.500;AN=2;Base
+QRankSum=2.43;ClippingRankSum=0.00;DP=11;ExcessHet=3.0103;FS=3.090;ML
+EAC=1;MLEAF=0.500;MQ=28.67;MQRankSum=-1.513e+00;QD=10.80;ReadPosRankS
+um=0.357;SOR=1.981 GT:AD:DP:GQ:PGT:PID:PL 0/1:7,4:11:99:0|1:145
+90_G_A:147,0,307 chr1 14590 14590 G A ncRNA_exonic
+ WASH7P intergenic NONE,MIR6859-3 dist=NONE;di
+st=2779
+
+
+
+ chr1:14590:14590:G:A 1 0.5 2.43
+ 0 11 no_DS no_END 3.0103 3.09 no_HaplotypeScore
+ no_InbreedingCoeff 1 0.5 28.67 -1.51E+00 10.8 no_
+RAW_MQ 0.357 1.981 CAAGCCAGCCTTCCGCTCCTTGAAGCTGGTCTCCACACAGT
+GCTGGTTCC[G]TCACCCCCTCCCAAGGAAGTAGGTCTGAGCAGCTTGTCCTGGCTGTGTCC pas
+s XX . 0 1 0
...
chr1 16949 . A C 183.77 . AC=1;AF=0.500;AN=2;Base
+QRankSum=-7.580e-01;ClippingRankSum=0.00;DP=31;ExcessHet=3.0103;FS=0.
+000;MLEAC=1;MLEAF=0.500;MQ=21.07;MQRankSum=-1.095e+00;QD=5.93;ReadPos
+RankSum=-3.240e-01;SOR=0.515 GT:AD:DP:GQ:PL 0/1:19,12:31:99:212
+,0,396 chr1 16949 16949 A C ncRNA_exonic WASH7P
+ downstream MIR6859-3 rs199745162
+0.0139776 0.0227 0.0144 0.0143 0.0159
+
+
+
+ 0.0159444 415 26028 chr1:16949:1694
+9:A:C 1 0.5 -7.58E-01 0 31 no_DS no_END 3.010
+3 0 no_HaplotypeScore no_InbreedingCoeff 1 0.5 21.0
+7 -1.10E+00 5.93 no_RAW_MQ -3.24E-01 0.515 CTGGAATG
+GTGCCAGGGGCAGAGGGGGCAATGCCGGGGCCCAGGTCGGCA[A]TGTACATGAGGTCGTTGGCAATGC
+CGGGCAGGTCAGGCAGGTAGGATGGA pass XX . 0 1 0
chr1 17020 . G A 99.77 . AC=1;AF=0.500;AN=2;BaseQ
+RankSum=-1.024e+00;ClippingRankSum=0.00;DP=26;ExcessHet=3.0103;FS=14.
+474;MLEAC=1;MLEAF=0.500;MQ=21.00;MQRankSum=0.00;QD=3.84;ReadPosRankSu
+m=-2.034e+00;SOR=2.800 GT:AD:DP:GQ:PL 0/1:18,8:26:99:128,0,424
+ chr1 17020 17020 G A ncRNA_exonic WASH7P
+ downstream MIR6859-3 rs199740902
+
+
+
+ 0.0141002 367
+ 26028 chr1:17020:17020:G:A 1 0.5 -1.02E+00 0 2
+6 no_DS no_END 3.0103 14.474 no_HaplotypeScore no_I
+nbreedingCoeff 1 0.5 21 0 3.84 no_RAW_MQ -2.03E+
+00 2.8 ATGCCGGGCAGGTCAGGCAGGTAGGATGGAACATCAATCTCAGGCACCTG[G]CCC
+AGGTCTGGCACATAGAAGTAGTTCTCTGGGACCTGCAAGATTAGGCA pass XX .
+ 0 1 0
chr1 17365 . C G 154.77 . AC=1;AF=0.500;AN=2;Base
+QRankSum=0.621;ClippingRankSum=0.00;DP=43;ExcessHet=3.0103;FS=0.000;M
+LEAC=1;MLEAF=0.500;MQ=43.91;MQRankSum=-1.245e+00;QD=3.60;ReadPosRankS
+um=-1.701e+00;SOR=0.485 GT:AD:DP:GQ:PGT:PID:PL 0/1:36,7:43:99:0
+|1:17365_C_G:183,0,2051 chr1 17365 17365 C G ncRNA_
+exonic WASH7P downstream MIR6859-3
+ rs369606208 0.2553 0.1603
+ 0.221 0.3841 0.2245 0.2715 0.2581 0.2883
+
+
+ 7.76E-05 12
+ 154602 chr1:17365:17365:C:G 1 0.5 0.621 0 43
+ no_DS no_END 3.0103 0 no_HaplotypeScore no_Inbreedin
+gCoeff 1 0.5 43.91 -1.25E+00 3.6 no_RAW_MQ -1.70
+E+00 0.485 TGGGTCTTTGTTACAGCACCAGCCAGGGGGTCCAGGAAGACATACTTCTT[C
+]TACCTACAGAGGCGACATGGGGGTCAGGCAAGCTGACACCCGCTGTCCTG pass XX
+. 0 1 0