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Uploaded tarball. Version 1.1. - Added stranded output. - Added, tested no-filter mode. - now prints all sites. - Changed handling of minor allele ties. - Added test datasets. - Revised help text.
author nick
date Fri, 06 Sep 2013 20:37:07 -0400
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##fileformat=VCFv4.1
##comment="ARGS=-f 0.2 -c 5000 -H -s"
##fileDate=20130521
##source=Dan
##reference=file:///scratch/dan/galaxy/galaxy-central/database/files/002/dataset_2536.dat
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##FORMAT=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##FORMAT=<ID=NC,Number=.,Type=String,Description="Nucleotide and indel counts">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	S1	S2	S3	S4
chrM	1000	.	ACTC	TCTC,CCTC,GCTC,ATC,A	.	.	AC=188032,682,8,8,1;AF=0.995310134556,0.00361003186568,4.23464148467e-05,4.23464148467e-05,5.29330185583e-06	GT:AC:AF:NC	1/1:12546,51,0,0,0:0.994688020297,0.00404344723698,0,0,0:+A=2,+C=20,+T=8020,-A=14,-C=31,-T=4526,	1/1:9970,38,1,1,0:0.995208624476,0.00379317228988,9.98203234178e-05,9.98203234178e-05,0:+A=1,+d1=1,+C=21,+T=6546,+G=1,-A=7,-C=17,-T=3424,	1/1:11372,35,0,2,0:0.995448179272,0.0030637254902,0,0.000175070028011,0:+d1=2,+C=10,+T=7199,-A=15,-C=25,-T=4173,	1/1:9115,39,0,0,0:0.995304651671,0.00425857174055,0,0,0:+C=13,+T=5817,-A=4,-C=26,-T=3298,
chrM	2000	.	TAC	CAC,AAC,GAC,T,TC,TGAC	.	.	AC=209371,114,8,2,2,1;AF=0.999083807733,0.000543989158392,3.81746777819e-05,9.54366944547e-06,9.54366944547e-06,4.77183472273e-06	GT:AC:AF:NC	1/1:14903,8,1,0,0,0:0.999329444109,0.000536444712667,6.70555890834e-05,0,0,0:+A=1,+C=9095,+G=1,-A=7,-C=5808,-T=1,	1/1:11838,3,0,0,0,0:0.999324666554,0.000253250042208,0,0,0,0:+C=7242,+T=4,-A=3,-C=4596,-T=1,	1/1:13175,10,1,0,0,0:0.998711340206,0.000758035172832,7.58035172832e-05,0,0,0:+C=7933,+T=4,-A=10,-C=5242,-T=2,-G=1,	1/1:10921,3,2,0,0,1:0.999176578225,0.000274473924977,0.000182982616651,0,0,9.14913083257e-05:+A=1,+TG=1,+C=6732,+T=1,-A=2,-C=4189,-T=2,-G=2,
chrM	3000	.	TC	AC,GC,CC,T,TGC	.	.	AC=386813,649,441,35,33;AF=0.996740346013,0.00167234421946,0.00113636949273,9.01880549786e-05,8.5034451837e-05	GT:AC:AF:NC	1/1:27966,44,42,5,6:0.996117542297,0.00156723063224,0.00149599287622,0.000178094390027,0.000213713268032:+A=17399,+d1=1,+C=7,+T=8,+G=22,-A=10567,-d1=4,-C=35,-G=22,-T=4,-TG=6,	1/1:20472,36,16,0,0:0.997272018706,0.00175370226033,0.000779423226812,0,0:+A=12535,+C=3,+T=2,+G=24,-A=7937,-C=13,-T=2,-G=12,	1/1:30267,46,40,5,3:0.996575680748,0.00151460274604,0.00131704586612,0.000164630733265,9.87784399592e-05:+A=18981,+d1=2,+C=7,+T=6,+G=29,-A=11286,-d1=3,-C=33,-G=17,-T=4,-TG=3,	1/1:15494,29,17,2,3:0.996526884487,0.00186519166452,0.00109338821713,0.000128633907898,0.000192950861847:+A=9254,+d1=2,+C=1,+T=2,+G=15,-A=6240,-TG=3,-C=16,-T=1,-G=14,
chrM	4000	.	TA	AA,GA,CA,T,TCA,TTA	.	.	AC=138825,77,37,9,8,3;AF=0.998511134127,0.000553829334254,0.000266125783992,6.47332988089e-05,5.75407100524e-05,2.15777662696e-05	GT:AC:AF:NC	1/1:12258,2,3,1,1,2:0.998940591639,0.00016298590172,0.000244478852579,8.14929508598e-05,8.14929508598e-05,0.00016298590172:+A=6134,+d1=1,+C=2,+G=1,+TT=1,+T=3,+TC=1,-A=6124,-C=1,-TT=1,-G=1,-T=1,	1/1:8934,6,3,0,0,0:0.998546998994,0.000670615848888,0.000335307924444,0,0,0:+A=4382,+T=3,+G=5,-A=4552,-C=3,-T=1,-G=1,	1/1:10135,4,1,2,1,0:0.999014292755,0.000394282897979,9.85707244948e-05,0.00019714144899,9.85707244948e-05,0:+A=4966,+d1=1,+TC=1,+G=3,-A=5169,-d1=1,-C=1,-T=2,-G=1,	1/1:7342,4,1,0,0,0:0.999183451279,0.000544365813827,0.000136091453457,0,0,0:+A=3711,+T=1,-A=3631,-C=1,-G=4,
chrM	5000	.	A	G,T,C	.	.	AC=28,27,10;AF=0.000251195421066,0.000242224156028,8.97126503808e-05	GT:AC:AF:NC	0/0:2,1,0:0.000190912562047,9.54562810233e-05,0:+A=3664,+T=1,-A=6809,-G=2,	0/0:7,1,2:0.000987724001693,0.000141103428813,0.000282206857627:+A=2337,+C=1,+T=1,+G=2,-A=4740,-C=1,-G=5,	0/0:2,3,0:0.00022411474675,0.000336172120126,0:+A=3194,+T=1,-A=5725,-T=2,-G=2,	0/0:1,1,0:0.000169865806013,0.000169865806013,0:+A=2022,+T=1,-A=3863,-G=1,
chrM	6000	.	T	C,A,TT,TCTTA,G	.	.	AC=118279,31,7,1,1;AF=0.999459199108,0.000261950432218,5.91500975977e-05,8.45001394252e-06,8.45001394252e-06	GT:AC:AF:NC	1/1:9612,2,0,0,1:0.999168399168,0.0002079002079,0,0,0.00010395010395:+C=4845,+T=3,-A=2,-C=4767,-T=2,-G=1,	1/1:7771,0,1,0,0:0.99987133299,0,0.000128667009779,0,0:+C=3682,-C=4089,-TT=1,	1/1:9152,1,0,0,0:0.999563128003,0.000109217999126,0,0,0:+C=4640,+T=1,-A=1,-C=4512,-T=2,	1/1:5500,0,1,0,0:0.99981821487,0,0.000181785129976,0,0:+C=2707,-C=2793,-TT=1,
chrM	7000	.	GTA	TTA,CTA,ATA,GA,GACTACTA,G	.	.	AC=177915,270,72,20,3,1;AF=0.997370840434,0.00151358866266,0.000403623643376,0.000112117678716,1.68176518073e-05,5.60588393578e-06	GT:AC:AF:NC	1/1:13745,26,4,1,0,0:0.997532476958,0.0018869293853,0.000290296828507,7.25742071268e-05,0,0:+d1=1,+C=17,+T=6216,+G=1,-A=4,-C=9,-T=7529,-G=2,	1/1:11392,16,0,1,0,0:0.997985107315,0.00140166447657,0,8.76040297854e-05,0,0:+d1=1,+C=7,+T=5104,+G=2,-C=9,-T=6288,-G=4,	1/1:13952,13,4,0,0,0:0.998068531368,0.000929966378139,0.000286143500966,0,0,0:+C=9,+T=6446,-A=4,-C=4,-T=7506,-G=10,	1/1:7740,12,1,0,0,0:0.998194480268,0.0015475883415,0.000128965695125,0,0,0:+C=8,+T=3471,-A=1,-C=4,-T=4269,-G=1,
chrM	8000	.	TGA	GGA,AGA,CGA,T	.	.	AC=132300,33,7,2;AF=0.999350384482,0.000249271070959,5.28756817186e-05,1.51073376339e-05	GT:AC:AF:NC	1/1:10337,2,0,2:0.999226679555,0.000193330111165,0,0.000193330111165:+A=1,+d2=1,+T=1,+G=4832,-A=1,-d2=1,-T=3,-G=5505,	1/1:8347,3,0,0:0.999640718563,0.000359281437126,0,0:+A=2,+G=4258,-A=1,-G=4089,	1/1:10066,4,1,0:0.999205876514,0.000397061743101,9.92654357753e-05,0:+A=3,+C=1,+T=1,+G=5023,-A=1,-T=2,-G=5043,	1/1:4891,2,3,0:0.99897875817,0.000408496732026,0.000612745098039,0:+A=1,+C=1,+G=1746,-A=1,-C=2,-G=3145,
chrM	9000	.	TACGC	AACGC,GACGC,CACGC,T,TCGACGC	.	.	AC=125089,77,46,8,2;AF=0.998842167463,0.000614849002667,0.000367312391204,6.38804158615e-05,1.59701039654e-05	GT:AC:AF:NC	1/1:10775,9,6,1,0:0.998517282921,0.000834028356964,0.000556018904643,9.26698174405e-05,0:+A=6306,+G=1,-A=4469,-C=6,-d4=1,-G=8,	1/1:8081,7,2,0,0:0.998764058831,0.00086515881844,0.00024718823384,0,0:+A=4777,+T=1,+G=3,-A=3304,-C=2,-G=4,	1/1:9475,4,3,2,0:0.998735111205,0.000421629598398,0.000316222198798,0.000210814799199,0:+A=5435,+G=1,-A=4040,-C=3,-d4=2,-T=3,-G=3,	1/1:5709,3,1,0,0:0.999299842465,0.000525118151584,0.000175039383861,0,0:+A=3234,+G=1,-A=2475,-C=1,-G=2,
#chrM	10000	.	AGT	GGT,TGT,AAGT,ACGT,A,CGT,AAGAGT,AACAGT,AT	.	.	AC=88942,145,51,12,7,6,5,2,1;AF=0.997051734768,0.00162546942436,0.000571716832016,0.000134521607533,7.84709377277e-05,6.72608037666e-05,5.60506698055e-05,2.24202679222e-05,1.12101339611e-05	GT:AC:AF:NC	1/1:7632,14,4,3,1,1,0,0,0:0.996735013713,0.00182839232075,0.000522397805929,0.000391798354447,0.000130599451482,0.000130599451482,0,0,0:+A=1,+C=1,+AC=3,+G=2535,+T=11,-A=1,-AA=4,-d2=1,-T=3,-G=5097,	1/1:6053,5,2,1,0,0,1,0,0:0.998186015831,0.000824538258575,0.00032981530343,0.000164907651715,0,0,0.000164907651715,0,0:+AC=1,+T=5,+G=1674,-A=2,-AA=2,-G=4379,-AAGA=1,	1/1:7012,14,6,0,2,0,0,0,0:0.996730632552,0.00199004975124,0.000852878464819,0,0.000284292821606,0,0,0,0:+d2=1,+T=11,+G=2241,-A=1,-AA=6,-d2=1,-T=3,-G=4771,	1/1:4646,1,2,0,0,0,0,0,0:0.998710232158,0.000214961306965,0.000429922613929,0,0,0,0,0,0:+A=1,+T=1,+G=1337,-A=2,-AA=2,-G=3309,
#chrM	11000	.	CCA	ACA,GCA,TCA,CA,C	.	.	AC=54,44,36,3,2;AF=0.000362343152385,0.00029524256861,0.00024156210159,2.01301751325e-05,1.3420116755e-05	GT:AC:AF:NC	0/0:7,3,1,0,0:0.000521920668058,0.000223680286311,7.45600954369e-05,0,0:+C=10229,+T=1,-A=7,-C=3172,-G=3,	0/0:3,4,2,0,0:0.000368233705659,0.000490978274211,0.000245489137106,0,0:+A=2,+C=6575,+T=2,+G=1,-A=1,-C=1563,-G=3,	0/0:9,3,2,0,0:0.000811615114077,0.000270538371359,0.000180358914239,0,0:+A=1,+C=7906,+T=2,-A=8,-C=3169,-G=3,	0/0:0,2,3,1,0:0,0.000220507166483,0.000330760749724,0.000110253583241,0:+d1=1,+C=7066,+T=2,-C=1998,-T=1,-G=2,
#chrM	12000	.	AC	CC,TC,GC,A	.	.	AC=182586,84,23,1;AF=0.999146337459,0.000459664444955,0.000125860502785,5.47219577328e-06	GT:AC:AF:NC	1/1:13592,8,0,0:0.999264813998,0.000588148801647,0,0:+A=2,+C=7113,+T=5,-C=6479,-T=3,	1/1:9868,1,0,0:0.999797365755,0.000101317122594,0,0:+C=5182,-A=1,-C=4686,-T=1,	1/1:11289,6,3,0:0.998938147067,0.000530926466684,0.000265463233342,0:+A=2,+C=6123,+T=3,+G=1,-A=1,-C=5166,-T=3,-G=2,	1/1:9708,4,0,0:0.999382334775,0.000411776816965,0,0:+A=1,+C=4892,+T=2,-A=1,-C=4816,-T=2,
#chrM	13000	.	A	G,C,T	.	.	AC=56125,9,6;AF=0.999358985773,0.000160253556739,0.000106835704492	GT:AC:AF:NC	1/1:3816,0,0:0.999214454046,0,0:+A=1,+G=1319,-A=2,-G=2497,	1/1:2814,1,0:0.999289772727,0.000355113636364,0:+G=986,-A=1,-C=1,-G=1828,	1/1:3479,0,0:0.999712643678,0,0:+A=1,+G=1285,-G=2194,	1/1:2679,0,0:1.0,0,0:+G=979,-G=1700,
#chrM	14000	.	CTAA	TTAA,GTAA,CAA,ATAA,C	.	.	AC=147853,32,22,21,1;AF=0.997766290558,0.000215947740647,0.000148464071695,0.000141715704799,6.74836689521e-06	GT:AC:AF:NC	1/1:10992,3,2,4,0:0.996825972613,0.000272059490342,0.000181372993561,0.000362745987123,0:+A=1,+d1=1,+C=19,+T=7038,-A=3,-d1=1,-C=7,-T=3954,-G=3,	1/1:6853,2,2,0,0:0.997525473071,0.000291120815138,0.000291120815138,0,0:+d1=2,+C=9,+T=4609,-C=4,-T=2244,-G=2,	1/1:9277,2,0,5,0:0.998063474987,0.000215169445939,0,0.000537923614847,0:+A=2,+C=9,+T=5786,-A=3,-C=2,-T=3491,-G=2,	1/1:8125,1,3,2,0:0.997422047631,0.000122759636631,0.000368278909894,0.000245519273263,0:+d1=2,+C=9,+T=5241,-A=2,-d1=1,-C=6,-T=2884,-G=1,
#chrM	15000	.	AA	GA,TA,CA,A	.	.	AC=132,29,29,4;AF=0.000611470633196,0.000134338245172,0.000134338245172,1.85294131272e-05	GT:AC:AF:NC	0/0:15,2,0,0:0.000956510649152,0.00012753475322,0,0:+A=8715,+T=1,+G=5,-A=6950,-T=1,-G=10,	0/0:13,1,0,0:0.00121985549404,9.38350380032e-05,0,0:+A=6102,+T=1,+G=6,-A=4541,-G=7,	0/0:1,2,5,1:7.86101721563e-05,0.000157220344313,0.000393050860781,7.86101721563e-05:+A=7378,+C=5,+T=2,-A=5334,-d1=1,-G=1,	0/0:6,0,0,0:0.000532765050613,0,0,0:+A=6215,+G=4,-A=5041,-G=2,
#chrM	16000	.	AG	GG,TG,CG,A	.	.	AC=224750,90,3,1;AF=0.999244175707,0.000400142272808,1.33380757603e-05,4.44602525342e-06	GT:AC:AF:NC	1/1:15911,2,0,0:0.99949745587,0.000125636032414,0,0:+A=3,+T=1,+G=7156,-A=3,-T=1,-G=8755,	1/1:11311,2,0,0:0.999381516169,0.000176709666019,0,0:+A=3,+G=4973,-A=2,-T=2,-G=6338,	1/1:14157,2,0,0:0.999012066897,0.000141133300402,0,0:+A=5,+T=1,+G=6766,-A=7,-T=1,-G=7391,	1/1:11039,3,0,0:0.999185372918,0.000271542360608,0,0:+A=4,+T=1,+G=4959,-A=2,-T=2,-G=6080,