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changeset 0:bfc76c3d5910 draft default tip

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Uploaded
author anton
date Mon, 15 Sep 2014 14:57:13 -0400
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files test-data/vcfflatten-input1.vcf test-data/vcfflatten-test1.vcf tool_dependencies.xml vcfflatten.xml
diffstat 4 files changed, 276 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/vcfflatten-input1.vcf	Mon Sep 15 14:57:13 2014 -0400
@@ -0,0 +1,121 @@
+##fileformat=VCFv4.1
+##fileDate=20140610
+##source=Dan
+##reference=file:///galaxy/data/phiX/sam_index/phiX.fa
+##filter="AF > .001"
+##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	groupA	groupB
+phiX174	1015	.	A	C	0	.	AC=2;AF=0.0555555555556	GT:AC:AF:NC	0:0,2:0,0.2:A=8,C=2,G=1,	0:0,0:0,0:A=26,G=1,
+phiX174	1016	.	A	T	0	.	AC=2;AF=0.0555555555556	GT:AC:AF:NC	0:0:0:A=10,	0:2:0.0769230769231:A=24,T=2,
+phiX174	1038	.	A	C	0	.	AC=2;AF=0.046511627907	GT:AC:AF:NC	0:2:0.153846153846:A=11,C=2,	0:0:0:A=30,
+phiX174	1045	.	T	G	0	.	AC=2;AF=0.0425531914894	GT:AC:AF:NC	0:0:0:T=15,G=1,	0:2:0.0625:T=30,G=2,
+phiX174	1048	.	C	A	0	.	AC=2;AF=0.0434782608696	GT:AC:AF:NC	0:2:0.133333333333:A=2,C=13,	0:0:0:C=31,G=1,
+phiX174	1050	.	A	C	0	.	AC=3;AF=0.0714285714286	GT:AC:AF:NC	0:0:0:A=12,	0:3:0.1:A=27,C=3,
+phiX174	1051	.	T	G	0	.	AC=2;AF=0.0487804878049	GT:AC:AF:NC	0:2:0.166666666667:C=1,T=10,G=2,	0:0:0:T=29,G=1,
+phiX174	1054	.	T	G	0	.	AC=2;AF=0.0454545454545	GT:AC:AF:NC	0:2:0.153846153846:T=11,G=2,	0:0:0:T=31,G=1,
+phiX174	1076	.	G	C	0	.	AC=2;AF=0.0363636363636	GT:AC:AF:NC	0:2:0.105263157895:A=1,C=2,G=17,	0:0:0:G=36,
+phiX174	1080	.	G	C	0	.	AC=2;AF=0.0344827586207	GT:AC:AF:NC	0:2:0.105263157895:A=1,C=2,T=1,G=17,	0:0:0:C=1,G=39,
+phiX174	1092	.	T	G	0	.	AC=2;AF=0.0263157894737	GT:AC:AF:NC	0:2:0.0833333333333:C=1,T=22,G=2,	0:0:0:T=52,G=1,
+phiX174	1093	.	T	G	0	.	AC=2;AF=0.025974025974	GT:AC:AF:NC	0:2:0.08:T=23,G=2,	0:0:0:T=52,
+phiX174	1102	.	T	C	0	.	AC=6;AF=0.0779220779221	GT:AC:AF:NC	0:2:0.0869565217391:C=2,T=21,	0:4:0.0740740740741:C=4,T=50,
+phiX174	1107	.	T	G	0	.	AC=2;AF=0.0277777777778	GT:AC:AF:NC	0:0:0:T=22,G=1,	0:2:0.04:T=48,G=2,
+phiX174	1110	.	T	C	0	.	AC=2;AF=0.0277777777778	GT:AC:AF:NC	0:2:0.125:C=2,T=14,	0:0:0:C=1,T=56,G=1,
+phiX174	1121	.	T	G	0	.	AC=3;AF=0.041095890411	GT:AC:AF:NC	0:0:0:T=19,	0:3:0.0555555555556:T=51,G=3,
+phiX174	1124	.	T	C	0	.	AC=2;AF=0.0307692307692	GT:AC:AF:NC	0:0,2:0,0.117647058824:C=2,T=15,G=1,	0:0,0:0,0:T=48,G=1,
+phiX174	1125	.	T	G	0	.	AC=3;AF=0.0454545454545	GT:AC:AF:NC	0:3:0.176470588235:T=14,G=3,	0:0:0:T=49,G=1,
+phiX174	1131	.	T	G	0	.	AC=2;AF=0.025641025641	GT:AC:AF:NC	0:2:0.0952380952381:T=19,G=2,	0:0:0:T=57,
+phiX174	1141	.	T	G	0	.	AC=2;AF=0.0253164556962	GT:AC:AF:NC	0:0:0:T=20,G=1,	0:2:0.0338983050847:T=57,G=2,
+phiX174	1145	.	G	C	0	.	AC=2;AF=0.027397260274	GT:AC:AF:NC	0:2:0.0952380952381:C=2,G=19,	0:0:0:G=52,
+phiX174	1147	.	T	C	0	.	AC=2;AF=0.0281690140845	GT:AC:AF:NC	0:2:0.0952380952381:C=2,T=19,	0:0:0:T=50,
+phiX174	1149	.	T	G,C	0	.	AC=2,2;AF=0.027027027027,0.027027027027	GT:AC:AF:NC	0:2,2:0.1,0.1:C=2,T=16,G=2,	0:0,0:0,0:T=54,
+phiX174	1156	.	T	G	0	.	AC=2;AF=0.031746031746	GT:AC:AF:NC	0:0:0:C=1,T=15,	0:2:0.0416666666667:T=46,G=2,
+phiX174	1159	.	T	C,G	0	.	AC=2,2;AF=0.0298507462687,0.0298507462687	GT:AC:AF:NC	0:2,0:0.111111111111,0:C=2,T=16,	0:0,2:0,0.0408163265306:C=1,T=47,G=2,
+phiX174	1164	.	T	G	0	.	AC=4;AF=0.0666666666667	GT:AC:AF:NC	0:0:0:C=1,T=16,G=1,	0:4:0.0909090909091:T=40,G=4,
+phiX174	1168	.	T	G	0	.	AC=4;AF=0.0666666666667	GT:AC:AF:NC	0:2:0.0952380952381:C=1,T=19,G=2,	0:2:0.0512820512821:T=37,G=2,
+phiX174	1171	.	T	G	0	.	AC=2;AF=0.0327868852459	GT:AC:AF:NC	0:2:0.0869565217391:T=21,G=2,	0:0:0:T=38,G=1,
+phiX174	1174	.	C	A	0	.	AC=2;AF=0.0327868852459	GT:AC:AF:NC	0:2:0.0869565217391:A=2,C=21,	0:0:0:A=1,C=38,
+phiX174	1178	.	G	C	0	.	AC=2;AF=0.0307692307692	GT:AC:AF:NC	0:2:0.0740740740741:C=2,T=1,G=25,	0:0:0:G=38,
+phiX174	1187	.	T	G	0	.	AC=3;AF=0.04	GT:AC:AF:NC	0:3:0.0882352941176:C=1,T=31,G=3,	0:0:0:T=41,
+phiX174	1189	.	T	C	0	.	AC=3;AF=0.0379746835443	GT:AC:AF:NC	0:3:0.0857142857143:C=3,T=32,G=1,	0:0:0:T=44,
+phiX174	1200	.	T	G	0	.	AC=3;AF=0.0365853658537	GT:AC:AF:NC	0:3:0.0882352941176:T=31,G=3,	0:0:0:T=48,G=1,
+phiX174	1202	.	T	G	0	.	AC=3;AF=0.0365853658537	GT:AC:AF:NC	0:0:0:T=32,	0:3:0.06:T=47,G=3,
+phiX174	1205	.	A	C	0	.	AC=2;AF=0.0246913580247	GT:AC:AF:NC	0:2:0.0588235294118:A=32,C=2,	0:0:0:A=47,C=1,G=1,
+phiX174	1207	.	T	G	0	.	AC=2;AF=0.0246913580247	GT:AC:AF:NC	0:0:0:A=1,T=34,	0:2:0.0425531914894:T=45,G=2,
+phiX174	1214	.	G	A	0	.	AC=2;AF=0.0246913580247	GT:AC:AF:NC	0:0:0:T=1,G=34,	0:2:0.0425531914894:A=2,G=45,
+phiX174	1216	.	C	A	0	.	AC=2;AF=0.0246913580247	GT:AC:AF:NC	0:0:0:C=34,	0:2:0.0425531914894:A=2,C=45,
+phiX174	1217	.	C	A	0	.	AC=2;AF=0.025	GT:AC:AF:NC	0:2:0.0588235294118:A=2,C=32,	0:0:0:C=46,
+phiX174	1219	.	T	G	0	.	AC=2;AF=0.025641025641	GT:AC:AF:NC	0:0:0:C=1,T=33,G=1,	0:2:0.0444444444444:T=43,G=2,
+phiX174	1223	.	C	T	0	.	AC=2;AF=0.025	GT:AC:AF:NC	0:2:0.0555555555556:C=34,T=2,	0:0:0:C=44,
+phiX174	1227	.	A	C	0	.	AC=2;AF=0.027027027027	GT:AC:AF:NC	0:2:0.0588235294118:A=32,C=2,	0:0:0:A=40,
+phiX174	1232	.	T	G	0	.	AC=2;AF=0.0298507462687	GT:AC:AF:NC	0:0:0:T=34,	0:2:0.0606060606061:C=1,T=31,G=2,
+phiX174	1236	.	G	T	0	.	AC=2;AF=0.0294117647059	GT:AC:AF:NC	0:2:0.0606060606061:A=1,T=2,G=31,	0:0:0:G=35,
+phiX174	1237	.	T	G	0	.	AC=2;AF=0.0294117647059	GT:AC:AF:NC	0:2:0.0571428571429:A=1,T=33,G=2,	0:0:0:T=33,G=1,
+phiX174	1240	.	A	C	0	.	AC=2;AF=0.0294117647059	GT:AC:AF:NC	0:0,0:0,0:A=32,T=1,	0:0,2:0,0.0555555555556:A=34,C=2,T=1,
+phiX174	1245	.	G	T	0	.	AC=4;AF=0.0625	GT:AC:AF:NC	0:2:0.0666666666667:C=1,T=2,G=28,	0:2:0.0588235294118:T=2,G=32,
+phiX174	1247	.	A	T	0	.	AC=2;AF=0.031746031746	GT:AC:AF:NC	0:2:0.0714285714286:A=26,C=1,T=2,G=1,	0:0:0:A=35,
+phiX174	1250	.	A	C	0	.	AC=2;AF=0.0307692307692	GT:AC:AF:NC	0:2:0.0769230769231:A=24,C=2,	0:0:0:A=39,
+phiX174	1251	.	A	G	0	.	AC=3;AF=0.044776119403	GT:AC:AF:NC	0:0:0:A=29,	0:3:0.0789473684211:A=35,C=1,G=3,
+phiX174	1253	.	T	G	0	.	AC=4;AF=0.0526315789474	GT:AC:AF:NC	0:2:0.0645161290323:T=29,G=2,	0:2:0.0444444444444:T=43,G=2,
+phiX174	1257	.	T	G	0	.	AC=2;AF=0.0281690140845	GT:AC:AF:NC	0:0:0:T=26,	0:2:0.0444444444444:T=43,G=2,
+phiX174	1259	.	A	C	0	.	AC=2;AF=0.027397260274	GT:AC:AF:NC	0:0:0:A=28,T=1,	0:2:0.0444444444444:A=43,C=2,G=1,
+phiX174	1274	.	G	C	0	.	AC=2;AF=0.0240963855422	GT:AC:AF:NC	0:2:0.0512820512821:C=2,G=37,	0:0:0:G=44,
+phiX174	1277	.	A	C	0	.	AC=2;AF=0.025	GT:AC:AF:NC	0:2:0.05:A=38,C=2,	0:0:0:A=40,G=1,
+phiX174	1279	.	T	G	0	.	AC=2;AF=0.0253164556962	GT:AC:AF:NC	0:0:0:T=39,G=1,	0:2:0.05:C=1,T=38,G=2,
+phiX174	1284	.	T	G,C	0	.	AC=3,2;AF=0.038961038961,0.025974025974	GT:AC:AF:NC	0:3,2:0.075,0.05:C=2,T=35,G=3,	0:0,0:0,0:A=1,T=37,
+phiX174	1289	.	A	C	0	.	AC=3;AF=0.0454545454545	GT:AC:AF:NC	0:3:0.0789473684211:A=35,C=3,	0:0:0:A=28,G=1,
+phiX174	1296	.	A	C	0	.	AC=2;AF=0.03125	GT:AC:AF:NC	0:0:0:A=38,	0:2:0.0769230769231:A=24,C=2,
+phiX174	1298	.	A	C	0	.	AC=3;AF=0.0491803278689	GT:AC:AF:NC	0:3,0:0.0810810810811,0:A=34,C=3,G=1,	0:0,0:0,0:A=24,C=1,T=1,G=1,
+phiX174	1306	.	T	G	0	.	AC=5;AF=0.0943396226415	GT:AC:AF:NC	0:5:0.178571428571:T=23,G=5,	0:0:0:C=1,T=25,
+phiX174	1307	.	T	G	0	.	AC=3;AF=0.0545454545455	GT:AC:AF:NC	0:3:0.107142857143:T=25,G=3,	0:0:0:C=1,T=27,
+phiX174	1314	.	A	G	0	.	AC=5;AF=0.0877192982456	GT:AC:AF:NC	0:2,0:0.0740740740741,0:A=25,C=1,G=2,	0:3,0:0.1,0:A=27,C=1,G=3,
+phiX174	1317	.	A	C	0	.	AC=2;AF=0.0322580645161	GT:AC:AF:NC	0:2:0.0740740740741:A=25,C=2,	0:0:0:A=35,
+phiX174	1320	.	C	G	0	.	AC=2;AF=0.0322580645161	GT:AC:AF:NC	0:2:0.0769230769231:C=24,G=2,	0:0:0:C=36,
+phiX174	1322	.	G	C	0	.	AC=3;AF=0.0441176470588	GT:AC:AF:NC	0:3:0.107142857143:C=3,G=25,	0:0:0:G=40,
+phiX174	1323	.	C	G	0	.	AC=2;AF=0.0298507462687	GT:AC:AF:NC	0:0:0:C=28,	0:2:0.0512820512821:C=37,T=1,G=2,
+phiX174	1329	.	T	C	0	.	AC=2;AF=0.0277777777778	GT:AC:AF:NC	0:2:0.0666666666667:C=2,T=28,	0:0:0:T=42,G=1,
+phiX174	1335	.	C	A	0	.	AC=2;AF=0.025974025974	GT:AC:AF:NC	0:2:0.0625:A=2,C=30,	0:0:0:C=45,
+phiX174	1338	.	T	A	0	.	AC=2;AF=0.027027027027	GT:AC:AF:NC	0:0:0:T=32,	0:2:0.047619047619:A=2,T=40,
+phiX174	1345	.	T	C	0	.	AC=2;AF=0.0253164556962	GT:AC:AF:NC	0:0,0:0,0:T=36,G=1,	0:0,2:0,0.046511627907:C=2,T=41,G=1,
+phiX174	1347	.	A	C	0	.	AC=2;AF=0.0243902439024	GT:AC:AF:NC	0:2:0.0512820512821:A=37,C=2,G=1,	0:0:0:A=43,
+phiX174	1348	.	T	G	0	.	AC=2;AF=0.0240963855422	GT:AC:AF:NC	0:2:0.05:T=38,G=2,	0:0:0:T=43,
+phiX174	1352	.	A	T	0	.	AC=2;AF=0.027397260274	GT:AC:AF:NC	0:0:0:A=34,G=1,	0:2:0.0512820512821:A=37,T=2,
+phiX174	1354	.	T	G,A	0	.	AC=2,2;AF=0.027027027027,0.027027027027	GT:AC:AF:NC	0:2,0:0.0526315789474,0:T=36,G=2,	0:0,2:0,0.0555555555556:A=2,T=34,G=1,
+phiX174	1359	.	T	G	0	.	AC=3;AF=0.0405405405405	GT:AC:AF:NC	0:3:0.0714285714286:T=39,G=3,	0:0:0:T=32,G=1,
+phiX174	1366	.	G	C	0	.	AC=3;AF=0.0428571428571	GT:AC:AF:NC	0:3:0.0714285714286:C=3,T=1,G=39,	0:0:0:G=28,
+phiX174	1370	.	T	G	0	.	AC=2;AF=0.0289855072464	GT:AC:AF:NC	0:0:0:C=1,T=45,G=1,	0:2:0.0833333333333:A=1,T=22,G=2,
+phiX174	1373	.	T	G	0	.	AC=2;AF=0.027027027027	GT:AC:AF:NC	0:2:0.0408163265306:T=47,G=2,	0:0:0:T=25,
+phiX174	1380	.	G	C	0	.	AC=2;AF=0.0238095238095	GT:AC:AF:NC	0:0,2:0,0.0384615384615:C=2,T=1,G=50,	0:0,0:0,0:T=1,G=32,
+phiX174	1381	.	T	G	0	.	AC=3;AF=0.0361445783133	GT:AC:AF:NC	0:3:0.0576923076923:A=1,T=49,G=3,	0:0:0:T=31,
+phiX174	1384	.	T	G	0	.	AC=4;AF=0.0512820512821	GT:AC:AF:NC	0:4:0.0816326530612:T=45,G=4,	0:0:0:T=29,G=1,
+phiX174	1385	.	T	G	0	.	AC=4;AF=0.0512820512821	GT:AC:AF:NC	0:4:0.0816326530612:T=45,G=4,	0:0:0:C=1,T=29,
+phiX174	1391	.	A	C	0	.	AC=2;AF=0.0253164556962	GT:AC:AF:NC	0:2:0.0408163265306:A=47,C=2,	0:0:0:A=30,C=1,
+phiX174	1393	.	C	A	0	.	AC=2;AF=0.0253164556962	GT:AC:AF:NC	0:2:0.0425531914894:A=2,C=45,	0:0:0:C=32,
+phiX174	1396	.	T	G	0	.	AC=3;AF=0.04	GT:AC:AF:NC	0:3:0.0697674418605:T=40,G=3,	0:0:0:T=32,
+phiX174	1397	.	A	C	0	.	AC=2;AF=0.027027027027	GT:AC:AF:NC	0:0:0:A=42,T=1,	0:2:0.0625:A=30,C=2,
+phiX174	1400	.	A	C	0	.	AC=2;AF=0.027397260274	GT:AC:AF:NC	0:2:0.047619047619:A=40,C=2,G=1,	0:0:0:A=31,
+phiX174	1401	.	A	C	0	.	AC=2;AF=0.027397260274	GT:AC:AF:NC	0:2:0.047619047619:A=40,C=2,	0:0:0:A=31,
+phiX174	1434	.	C	T	0	.	AC=2;AF=0.0571428571429	GT:AC:AF:NC	0:2:0.142857142857:C=12,T=2,	0:0:0:C=21,
+phiX174	1438	.	G	C	0	.	AC=2;AF=0.0526315789474	GT:AC:AF:NC	0:0:0:G=15,	0:2:0.0869565217391:C=2,G=21,
+phiX174	1450	.	T	G	0	.	AC=3;AF=0.0789473684211	GT:AC:AF:NC	0:3:0.176470588235:A=1,C=1,T=14,G=3,	0:0:0:T=21,G=1,
+phiX174	1459	.	T	G	0	.	AC=3;AF=0.075	GT:AC:AF:NC	0:3:0.142857142857:C=1,T=18,G=3,	0:0:0:T=19,
+phiX174	1470	.	C	A	0	.	AC=2;AF=0.0384615384615	GT:AC:AF:NC	0:0:0:C=29,	0:2:0.0869565217391:A=2,C=21,
+phiX174	1484	.	C	G	0	.	AC=2;AF=0.0384615384615	GT:AC:AF:NC	0:2:0.0740740740741:A=1,C=25,G=2,	0:0:0:C=25,
+phiX174	1487	.	T	G	0	.	AC=2;AF=0.0363636363636	GT:AC:AF:NC	0:2:0.0689655172414:T=27,G=2,	0:0:0:T=26,
+phiX174	1491	.	G	T	0	.	AC=2;AF=0.037037037037	GT:AC:AF:NC	0:0:0:T=1,G=26,	0:2:0.0714285714286:T=2,G=26,
+phiX174	1503	.	A	C	0	.	AC=2;AF=0.0454545454545	GT:AC:AF:NC	0:0:0:A=20,C=1,	0:2:0.0833333333333:A=22,C=2,
+phiX174	1536	.	A	C	0	.	AC=3;AF=0.0545454545455	GT:AC:AF:NC	0:3:0.111111111111:A=24,C=3,	0:0:0:A=28,C=1,
+phiX174	1541	.	T	G	0	.	AC=2;AF=0.0363636363636	GT:AC:AF:NC	0:2:0.0740740740741:T=25,G=2,	0:0:0:T=28,
+phiX174	1553	.	A	G	0	.	AC=2;AF=0.0408163265306	GT:AC:AF:NC	0:2:0.0952380952381:A=19,C=1,G=2,	0:0:0:A=28,
+phiX174	1566	.	C	G	0	.	AC=2;AF=0.0307692307692	GT:AC:AF:NC	0:0:0:C=30,T=1,	0:2:0.0571428571429:C=33,G=2,
+phiX174	1572	.	T	G	0	.	AC=2;AF=0.03125	GT:AC:AF:NC	0:2:0.0625:T=30,G=2,	0:0:0:T=32,
+phiX174	1574	.	G	C	0	.	AC=3;AF=0.0441176470588	GT:AC:AF:NC	0:3:0.0882352941176:C=3,G=31,	0:0:0:G=34,
+phiX174	1575	.	A	C	0	.	AC=2;AF=0.0294117647059	GT:AC:AF:NC	0:2:0.0571428571429:A=33,C=2,	0:0:0:A=33,T=1,
+phiX174	1577	.	A	C	0	.	AC=3;AF=0.0441176470588	GT:AC:AF:NC	0:0:0:A=35,	0:3:0.0909090909091:A=30,C=3,
+phiX174	1581	.	T	G	0	.	AC=2;AF=0.0285714285714	GT:AC:AF:NC	0:2:0.0555555555556:C=1,T=34,G=2,	0:0:0:T=34,G=1,
+phiX174	1591	.	A	C	0	.	AC=3;AF=0.037037037037	GT:AC:AF:NC	0:3:0.0789473684211:A=35,C=3,	0:0:0:A=43,C=1,
+phiX174	1597	.	T	G	0	.	AC=2;AF=0.025641025641	GT:AC:AF:NC	0:2:0.0606060606061:T=31,G=2,	0:0:0:C=1,T=45,
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/vcfflatten-test1.vcf	Mon Sep 15 14:57:13 2014 -0400
@@ -0,0 +1,121 @@
+##fileformat=VCFv4.1
+##fileDate=20140610
+##source=Dan
+##reference=file:///galaxy/data/phiX/sam_index/phiX.fa
+##filter="AF > .001"
+##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	groupA	groupB
+phiX174	1015	.	A	C	0	.	AC=2;AF=0.0555555555556	GT:AC:AF:NC	0:0,2:0,0.2:A=8,C=2,G=1,	0:0,0:0,0:A=26,G=1,
+phiX174	1016	.	A	T	0	.	AC=2;AF=0.0555555555556	GT:AC:AF:NC	0:0:0:A=10,	0:2:0.0769230769231:A=24,T=2,
+phiX174	1038	.	A	C	0	.	AC=2;AF=0.046511627907	GT:AC:AF:NC	0:2:0.153846153846:A=11,C=2,	0:0:0:A=30,
+phiX174	1045	.	T	G	0	.	AC=2;AF=0.0425531914894	GT:AC:AF:NC	0:0:0:T=15,G=1,	0:2:0.0625:T=30,G=2,
+phiX174	1048	.	C	A	0	.	AC=2;AF=0.0434782608696	GT:AC:AF:NC	0:2:0.133333333333:A=2,C=13,	0:0:0:C=31,G=1,
+phiX174	1050	.	A	C	0	.	AC=3;AF=0.0714285714286	GT:AC:AF:NC	0:0:0:A=12,	0:3:0.1:A=27,C=3,
+phiX174	1051	.	T	G	0	.	AC=2;AF=0.0487804878049	GT:AC:AF:NC	0:2:0.166666666667:C=1,T=10,G=2,	0:0:0:T=29,G=1,
+phiX174	1054	.	T	G	0	.	AC=2;AF=0.0454545454545	GT:AC:AF:NC	0:2:0.153846153846:T=11,G=2,	0:0:0:T=31,G=1,
+phiX174	1076	.	G	C	0	.	AC=2;AF=0.0363636363636	GT:AC:AF:NC	0:2:0.105263157895:A=1,C=2,G=17,	0:0:0:G=36,
+phiX174	1080	.	G	C	0	.	AC=2;AF=0.0344827586207	GT:AC:AF:NC	0:2:0.105263157895:A=1,C=2,T=1,G=17,	0:0:0:C=1,G=39,
+phiX174	1092	.	T	G	0	.	AC=2;AF=0.0263157894737	GT:AC:AF:NC	0:2:0.0833333333333:C=1,T=22,G=2,	0:0:0:T=52,G=1,
+phiX174	1093	.	T	G	0	.	AC=2;AF=0.025974025974	GT:AC:AF:NC	0:2:0.08:T=23,G=2,	0:0:0:T=52,
+phiX174	1102	.	T	C	0	.	AC=6;AF=0.0779220779221	GT:AC:AF:NC	0:2:0.0869565217391:C=2,T=21,	0:4:0.0740740740741:C=4,T=50,
+phiX174	1107	.	T	G	0	.	AC=2;AF=0.0277777777778	GT:AC:AF:NC	0:0:0:T=22,G=1,	0:2:0.04:T=48,G=2,
+phiX174	1110	.	T	C	0	.	AC=2;AF=0.0277777777778	GT:AC:AF:NC	0:2:0.125:C=2,T=14,	0:0:0:C=1,T=56,G=1,
+phiX174	1121	.	T	G	0	.	AC=3;AF=0.041095890411	GT:AC:AF:NC	0:0:0:T=19,	0:3:0.0555555555556:T=51,G=3,
+phiX174	1124	.	T	C	0	.	AC=2;AF=0.0307692307692	GT:AC:AF:NC	0:0,2:0,0.117647058824:C=2,T=15,G=1,	0:0,0:0,0:T=48,G=1,
+phiX174	1125	.	T	G	0	.	AC=3;AF=0.0454545454545	GT:AC:AF:NC	0:3:0.176470588235:T=14,G=3,	0:0:0:T=49,G=1,
+phiX174	1131	.	T	G	0	.	AC=2;AF=0.025641025641	GT:AC:AF:NC	0:2:0.0952380952381:T=19,G=2,	0:0:0:T=57,
+phiX174	1141	.	T	G	0	.	AC=2;AF=0.0253164556962	GT:AC:AF:NC	0:0:0:T=20,G=1,	0:2:0.0338983050847:T=57,G=2,
+phiX174	1145	.	G	C	0	.	AC=2;AF=0.027397260274	GT:AC:AF:NC	0:2:0.0952380952381:C=2,G=19,	0:0:0:G=52,
+phiX174	1147	.	T	C	0	.	AC=2;AF=0.0281690140845	GT:AC:AF:NC	0:2:0.0952380952381:C=2,T=19,	0:0:0:T=50,
+phiX174	1149	.	T	C	0	.	AC=2;AF=0.027027027027	GT:AC:AF:NC	0:2,2:0.1,0.1:C=2,T=16,G=2,	0:0,0:0,0:T=54,
+phiX174	1156	.	T	G	0	.	AC=2;AF=0.031746031746	GT:AC:AF:NC	0:0:0:C=1,T=15,	0:2:0.0416666666667:T=46,G=2,
+phiX174	1159	.	T	G	0	.	AC=2;AF=0.0298507462687	GT:AC:AF:NC	0:2,0:0.111111111111,0:C=2,T=16,	0:0,2:0,0.0408163265306:C=1,T=47,G=2,
+phiX174	1164	.	T	G	0	.	AC=4;AF=0.0666666666667	GT:AC:AF:NC	0:0:0:C=1,T=16,G=1,	0:4:0.0909090909091:T=40,G=4,
+phiX174	1168	.	T	G	0	.	AC=4;AF=0.0666666666667	GT:AC:AF:NC	0:2:0.0952380952381:C=1,T=19,G=2,	0:2:0.0512820512821:T=37,G=2,
+phiX174	1171	.	T	G	0	.	AC=2;AF=0.0327868852459	GT:AC:AF:NC	0:2:0.0869565217391:T=21,G=2,	0:0:0:T=38,G=1,
+phiX174	1174	.	C	A	0	.	AC=2;AF=0.0327868852459	GT:AC:AF:NC	0:2:0.0869565217391:A=2,C=21,	0:0:0:A=1,C=38,
+phiX174	1178	.	G	C	0	.	AC=2;AF=0.0307692307692	GT:AC:AF:NC	0:2:0.0740740740741:C=2,T=1,G=25,	0:0:0:G=38,
+phiX174	1187	.	T	G	0	.	AC=3;AF=0.04	GT:AC:AF:NC	0:3:0.0882352941176:C=1,T=31,G=3,	0:0:0:T=41,
+phiX174	1189	.	T	C	0	.	AC=3;AF=0.0379746835443	GT:AC:AF:NC	0:3:0.0857142857143:C=3,T=32,G=1,	0:0:0:T=44,
+phiX174	1200	.	T	G	0	.	AC=3;AF=0.0365853658537	GT:AC:AF:NC	0:3:0.0882352941176:T=31,G=3,	0:0:0:T=48,G=1,
+phiX174	1202	.	T	G	0	.	AC=3;AF=0.0365853658537	GT:AC:AF:NC	0:0:0:T=32,	0:3:0.06:T=47,G=3,
+phiX174	1205	.	A	C	0	.	AC=2;AF=0.0246913580247	GT:AC:AF:NC	0:2:0.0588235294118:A=32,C=2,	0:0:0:A=47,C=1,G=1,
+phiX174	1207	.	T	G	0	.	AC=2;AF=0.0246913580247	GT:AC:AF:NC	0:0:0:A=1,T=34,	0:2:0.0425531914894:T=45,G=2,
+phiX174	1214	.	G	A	0	.	AC=2;AF=0.0246913580247	GT:AC:AF:NC	0:0:0:T=1,G=34,	0:2:0.0425531914894:A=2,G=45,
+phiX174	1216	.	C	A	0	.	AC=2;AF=0.0246913580247	GT:AC:AF:NC	0:0:0:C=34,	0:2:0.0425531914894:A=2,C=45,
+phiX174	1217	.	C	A	0	.	AC=2;AF=0.025	GT:AC:AF:NC	0:2:0.0588235294118:A=2,C=32,	0:0:0:C=46,
+phiX174	1219	.	T	G	0	.	AC=2;AF=0.025641025641	GT:AC:AF:NC	0:0:0:C=1,T=33,G=1,	0:2:0.0444444444444:T=43,G=2,
+phiX174	1223	.	C	T	0	.	AC=2;AF=0.025	GT:AC:AF:NC	0:2:0.0555555555556:C=34,T=2,	0:0:0:C=44,
+phiX174	1227	.	A	C	0	.	AC=2;AF=0.027027027027	GT:AC:AF:NC	0:2:0.0588235294118:A=32,C=2,	0:0:0:A=40,
+phiX174	1232	.	T	G	0	.	AC=2;AF=0.0298507462687	GT:AC:AF:NC	0:0:0:T=34,	0:2:0.0606060606061:C=1,T=31,G=2,
+phiX174	1236	.	G	T	0	.	AC=2;AF=0.0294117647059	GT:AC:AF:NC	0:2:0.0606060606061:A=1,T=2,G=31,	0:0:0:G=35,
+phiX174	1237	.	T	G	0	.	AC=2;AF=0.0294117647059	GT:AC:AF:NC	0:2:0.0571428571429:A=1,T=33,G=2,	0:0:0:T=33,G=1,
+phiX174	1240	.	A	C	0	.	AC=2;AF=0.0294117647059	GT:AC:AF:NC	0:0,0:0,0:A=32,T=1,	0:0,2:0,0.0555555555556:A=34,C=2,T=1,
+phiX174	1245	.	G	T	0	.	AC=4;AF=0.0625	GT:AC:AF:NC	0:2:0.0666666666667:C=1,T=2,G=28,	0:2:0.0588235294118:T=2,G=32,
+phiX174	1247	.	A	T	0	.	AC=2;AF=0.031746031746	GT:AC:AF:NC	0:2:0.0714285714286:A=26,C=1,T=2,G=1,	0:0:0:A=35,
+phiX174	1250	.	A	C	0	.	AC=2;AF=0.0307692307692	GT:AC:AF:NC	0:2:0.0769230769231:A=24,C=2,	0:0:0:A=39,
+phiX174	1251	.	A	G	0	.	AC=3;AF=0.044776119403	GT:AC:AF:NC	0:0:0:A=29,	0:3:0.0789473684211:A=35,C=1,G=3,
+phiX174	1253	.	T	G	0	.	AC=4;AF=0.0526315789474	GT:AC:AF:NC	0:2:0.0645161290323:T=29,G=2,	0:2:0.0444444444444:T=43,G=2,
+phiX174	1257	.	T	G	0	.	AC=2;AF=0.0281690140845	GT:AC:AF:NC	0:0:0:T=26,	0:2:0.0444444444444:T=43,G=2,
+phiX174	1259	.	A	C	0	.	AC=2;AF=0.027397260274	GT:AC:AF:NC	0:0:0:A=28,T=1,	0:2:0.0444444444444:A=43,C=2,G=1,
+phiX174	1274	.	G	C	0	.	AC=2;AF=0.0240963855422	GT:AC:AF:NC	0:2:0.0512820512821:C=2,G=37,	0:0:0:G=44,
+phiX174	1277	.	A	C	0	.	AC=2;AF=0.025	GT:AC:AF:NC	0:2:0.05:A=38,C=2,	0:0:0:A=40,G=1,
+phiX174	1279	.	T	G	0	.	AC=2;AF=0.0253164556962	GT:AC:AF:NC	0:0:0:T=39,G=1,	0:2:0.05:C=1,T=38,G=2,
+phiX174	1284	.	T	G	0	.	AC=3;AF=0.038961038961	GT:AC:AF:NC	0:3,2:0.075,0.05:C=2,T=35,G=3,	0:0,0:0,0:A=1,T=37,
+phiX174	1289	.	A	C	0	.	AC=3;AF=0.0454545454545	GT:AC:AF:NC	0:3:0.0789473684211:A=35,C=3,	0:0:0:A=28,G=1,
+phiX174	1296	.	A	C	0	.	AC=2;AF=0.03125	GT:AC:AF:NC	0:0:0:A=38,	0:2:0.0769230769231:A=24,C=2,
+phiX174	1298	.	A	C	0	.	AC=3;AF=0.0491803278689	GT:AC:AF:NC	0:3,0:0.0810810810811,0:A=34,C=3,G=1,	0:0,0:0,0:A=24,C=1,T=1,G=1,
+phiX174	1306	.	T	G	0	.	AC=5;AF=0.0943396226415	GT:AC:AF:NC	0:5:0.178571428571:T=23,G=5,	0:0:0:C=1,T=25,
+phiX174	1307	.	T	G	0	.	AC=3;AF=0.0545454545455	GT:AC:AF:NC	0:3:0.107142857143:T=25,G=3,	0:0:0:C=1,T=27,
+phiX174	1314	.	A	G	0	.	AC=5;AF=0.0877192982456	GT:AC:AF:NC	0:2,0:0.0740740740741,0:A=25,C=1,G=2,	0:3,0:0.1,0:A=27,C=1,G=3,
+phiX174	1317	.	A	C	0	.	AC=2;AF=0.0322580645161	GT:AC:AF:NC	0:2:0.0740740740741:A=25,C=2,	0:0:0:A=35,
+phiX174	1320	.	C	G	0	.	AC=2;AF=0.0322580645161	GT:AC:AF:NC	0:2:0.0769230769231:C=24,G=2,	0:0:0:C=36,
+phiX174	1322	.	G	C	0	.	AC=3;AF=0.0441176470588	GT:AC:AF:NC	0:3:0.107142857143:C=3,G=25,	0:0:0:G=40,
+phiX174	1323	.	C	G	0	.	AC=2;AF=0.0298507462687	GT:AC:AF:NC	0:0:0:C=28,	0:2:0.0512820512821:C=37,T=1,G=2,
+phiX174	1329	.	T	C	0	.	AC=2;AF=0.0277777777778	GT:AC:AF:NC	0:2:0.0666666666667:C=2,T=28,	0:0:0:T=42,G=1,
+phiX174	1335	.	C	A	0	.	AC=2;AF=0.025974025974	GT:AC:AF:NC	0:2:0.0625:A=2,C=30,	0:0:0:C=45,
+phiX174	1338	.	T	A	0	.	AC=2;AF=0.027027027027	GT:AC:AF:NC	0:0:0:T=32,	0:2:0.047619047619:A=2,T=40,
+phiX174	1345	.	T	C	0	.	AC=2;AF=0.0253164556962	GT:AC:AF:NC	0:0,0:0,0:T=36,G=1,	0:0,2:0,0.046511627907:C=2,T=41,G=1,
+phiX174	1347	.	A	C	0	.	AC=2;AF=0.0243902439024	GT:AC:AF:NC	0:2:0.0512820512821:A=37,C=2,G=1,	0:0:0:A=43,
+phiX174	1348	.	T	G	0	.	AC=2;AF=0.0240963855422	GT:AC:AF:NC	0:2:0.05:T=38,G=2,	0:0:0:T=43,
+phiX174	1352	.	A	T	0	.	AC=2;AF=0.027397260274	GT:AC:AF:NC	0:0:0:A=34,G=1,	0:2:0.0512820512821:A=37,T=2,
+phiX174	1354	.	T	A	0	.	AC=2;AF=0.027027027027	GT:AC:AF:NC	0:2,0:0.0526315789474,0:T=36,G=2,	0:0,2:0,0.0555555555556:A=2,T=34,G=1,
+phiX174	1359	.	T	G	0	.	AC=3;AF=0.0405405405405	GT:AC:AF:NC	0:3:0.0714285714286:T=39,G=3,	0:0:0:T=32,G=1,
+phiX174	1366	.	G	C	0	.	AC=3;AF=0.0428571428571	GT:AC:AF:NC	0:3:0.0714285714286:C=3,T=1,G=39,	0:0:0:G=28,
+phiX174	1370	.	T	G	0	.	AC=2;AF=0.0289855072464	GT:AC:AF:NC	0:0:0:C=1,T=45,G=1,	0:2:0.0833333333333:A=1,T=22,G=2,
+phiX174	1373	.	T	G	0	.	AC=2;AF=0.027027027027	GT:AC:AF:NC	0:2:0.0408163265306:T=47,G=2,	0:0:0:T=25,
+phiX174	1380	.	G	C	0	.	AC=2;AF=0.0238095238095	GT:AC:AF:NC	0:0,2:0,0.0384615384615:C=2,T=1,G=50,	0:0,0:0,0:T=1,G=32,
+phiX174	1381	.	T	G	0	.	AC=3;AF=0.0361445783133	GT:AC:AF:NC	0:3:0.0576923076923:A=1,T=49,G=3,	0:0:0:T=31,
+phiX174	1384	.	T	G	0	.	AC=4;AF=0.0512820512821	GT:AC:AF:NC	0:4:0.0816326530612:T=45,G=4,	0:0:0:T=29,G=1,
+phiX174	1385	.	T	G	0	.	AC=4;AF=0.0512820512821	GT:AC:AF:NC	0:4:0.0816326530612:T=45,G=4,	0:0:0:C=1,T=29,
+phiX174	1391	.	A	C	0	.	AC=2;AF=0.0253164556962	GT:AC:AF:NC	0:2:0.0408163265306:A=47,C=2,	0:0:0:A=30,C=1,
+phiX174	1393	.	C	A	0	.	AC=2;AF=0.0253164556962	GT:AC:AF:NC	0:2:0.0425531914894:A=2,C=45,	0:0:0:C=32,
+phiX174	1396	.	T	G	0	.	AC=3;AF=0.04	GT:AC:AF:NC	0:3:0.0697674418605:T=40,G=3,	0:0:0:T=32,
+phiX174	1397	.	A	C	0	.	AC=2;AF=0.027027027027	GT:AC:AF:NC	0:0:0:A=42,T=1,	0:2:0.0625:A=30,C=2,
+phiX174	1400	.	A	C	0	.	AC=2;AF=0.027397260274	GT:AC:AF:NC	0:2:0.047619047619:A=40,C=2,G=1,	0:0:0:A=31,
+phiX174	1401	.	A	C	0	.	AC=2;AF=0.027397260274	GT:AC:AF:NC	0:2:0.047619047619:A=40,C=2,	0:0:0:A=31,
+phiX174	1434	.	C	T	0	.	AC=2;AF=0.0571428571429	GT:AC:AF:NC	0:2:0.142857142857:C=12,T=2,	0:0:0:C=21,
+phiX174	1438	.	G	C	0	.	AC=2;AF=0.0526315789474	GT:AC:AF:NC	0:0:0:G=15,	0:2:0.0869565217391:C=2,G=21,
+phiX174	1450	.	T	G	0	.	AC=3;AF=0.0789473684211	GT:AC:AF:NC	0:3:0.176470588235:A=1,C=1,T=14,G=3,	0:0:0:T=21,G=1,
+phiX174	1459	.	T	G	0	.	AC=3;AF=0.075	GT:AC:AF:NC	0:3:0.142857142857:C=1,T=18,G=3,	0:0:0:T=19,
+phiX174	1470	.	C	A	0	.	AC=2;AF=0.0384615384615	GT:AC:AF:NC	0:0:0:C=29,	0:2:0.0869565217391:A=2,C=21,
+phiX174	1484	.	C	G	0	.	AC=2;AF=0.0384615384615	GT:AC:AF:NC	0:2:0.0740740740741:A=1,C=25,G=2,	0:0:0:C=25,
+phiX174	1487	.	T	G	0	.	AC=2;AF=0.0363636363636	GT:AC:AF:NC	0:2:0.0689655172414:T=27,G=2,	0:0:0:T=26,
+phiX174	1491	.	G	T	0	.	AC=2;AF=0.037037037037	GT:AC:AF:NC	0:0:0:T=1,G=26,	0:2:0.0714285714286:T=2,G=26,
+phiX174	1503	.	A	C	0	.	AC=2;AF=0.0454545454545	GT:AC:AF:NC	0:0:0:A=20,C=1,	0:2:0.0833333333333:A=22,C=2,
+phiX174	1536	.	A	C	0	.	AC=3;AF=0.0545454545455	GT:AC:AF:NC	0:3:0.111111111111:A=24,C=3,	0:0:0:A=28,C=1,
+phiX174	1541	.	T	G	0	.	AC=2;AF=0.0363636363636	GT:AC:AF:NC	0:2:0.0740740740741:T=25,G=2,	0:0:0:T=28,
+phiX174	1553	.	A	G	0	.	AC=2;AF=0.0408163265306	GT:AC:AF:NC	0:2:0.0952380952381:A=19,C=1,G=2,	0:0:0:A=28,
+phiX174	1566	.	C	G	0	.	AC=2;AF=0.0307692307692	GT:AC:AF:NC	0:0:0:C=30,T=1,	0:2:0.0571428571429:C=33,G=2,
+phiX174	1572	.	T	G	0	.	AC=2;AF=0.03125	GT:AC:AF:NC	0:2:0.0625:T=30,G=2,	0:0:0:T=32,
+phiX174	1574	.	G	C	0	.	AC=3;AF=0.0441176470588	GT:AC:AF:NC	0:3:0.0882352941176:C=3,G=31,	0:0:0:G=34,
+phiX174	1575	.	A	C	0	.	AC=2;AF=0.0294117647059	GT:AC:AF:NC	0:2:0.0571428571429:A=33,C=2,	0:0:0:A=33,T=1,
+phiX174	1577	.	A	C	0	.	AC=3;AF=0.0441176470588	GT:AC:AF:NC	0:0:0:A=35,	0:3:0.0909090909091:A=30,C=3,
+phiX174	1581	.	T	G	0	.	AC=2;AF=0.0285714285714	GT:AC:AF:NC	0:2:0.0555555555556:C=1,T=34,G=2,	0:0:0:T=34,G=1,
+phiX174	1591	.	A	C	0	.	AC=3;AF=0.037037037037	GT:AC:AF:NC	0:3:0.0789473684211:A=35,C=3,	0:0:0:A=43,C=1,
+phiX174	1597	.	T	G	0	.	AC=2;AF=0.025641025641	GT:AC:AF:NC	0:2:0.0606060606061:T=31,G=2,	0:0:0:C=1,T=45,
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Sep 15 14:57:13 2014 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="vcflib" version="8a5602bf07">
+        <repository changeset_revision="bffe0495cd92" name="package_vcflib_8a5602bf07" owner="anton" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vcfflatten.xml	Mon Sep 15 14:57:13 2014 -0400
@@ -0,0 +1,28 @@
+<tool id="vcfflatten2" name="VCFflatten:" version="0.0.2">
+<requirements>
+    <requirement type="package" version="8a5602bf07">vcflib</requirement>
+</requirements>
+  <description>Removes multi-allelic sites by picking the most common alternate</description>
+  <command>vcfflatten "${input1}" > "${out_file1}"</command>
+  <inputs>
+    <param format="vcf" name="input1" type="data" label="Select VCF dataset"/>
+  </inputs>
+  <outputs>
+    <data format="vcf" name="out_file1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input1" value="vcfflatten-input1.vcf"/>
+      <output name="out_file1" file="vcfflatten-test1.vcf"/>
+    </test>
+    </tests>
+  <help>
+
+Removes multi-allelic sites by picking the most common alternate.  Requires allele frequency specification 'AF' and use of 'G' and 'A' to specify the fields which vary according to the Allele or Genotype.
+
+----
+
+Vcfflatten is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).                                                                                                                                 
+
+</help>
+</tool>