Mercurial > repos > jjohnson > bcftools_convert_from_vcf

diff test-data/annotate.vcf @ 0:d396503fdbdb draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
author jjohnson
date Sat, 25 Jun 2016 20:47:20 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotate.vcf	Sat Jun 25 20:47:20 2016 -0400
@@ -0,0 +1,39 @@
+##fileformat=VCFv4.1
+##INFO=<ID=TEST,Number=1,Type=Integer,Description="Testing Tag">
+##FORMAT=<ID=TT,Number=A,Type=Integer,Description="Testing Tag, with commas and \"escapes\" and escaped escapes combined with \\\"quotes\\\\\"">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood">
+##FILTER=<ID=q10,Description="Quality below 10">
+##FILTER=<ID=test,Description="Testing filter">
+##contig=<ID=1,assembly=b37,length=249250621>
+##contig=<ID=2,assembly=b37,length=249250621>
+##contig=<ID=3,assembly=b37,length=198022430>
+##contig=<ID=4,assembly=b37,length=191154276>
+##test=<ID=4,IE=5>
+##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
+##readme=AAAAAA
+##readme=BBBBBB
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=STR,Number=1,Type=String,Description="Test string type">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A	B
+1	3000150	.	C	T	59.2	PASS	AN=4;AC=2	GT:GQ	0/1:245	0/1:245
+1	3000151	.	C	T	59.2	PASS	AN=4;AC=2	GT:DP:GQ	0/1:32:245	0/1:32:245
+1	3062915	id3D	GTTT	G	12.9	q10	DP4=1,2,3,4;AN=4;AC=2;INDEL;STR=test	GT:GQ:DP:GL	0/1:409:35:-20,-5,-20	0/1:409:35:-20,-5,-20
+1	3062915	idSNP	G	T,C	12.6	test	TEST=5;DP4=1,2,3,4;AN=3;AC=1,1	GT:TT:GQ:DP:GL	0/1:0,1:409:35:-20,-5,-20,-20,-5,-20	2:0,1:409:35:-20,-5,-20
+1	3106154	.	CAAA	C	342	PASS	AN=4;AC=2	GT:GQ:DP	0/1:245:32	0/1:245:32
+1	3106154	.	C	CT	59.2	PASS	AN=4;AC=2	GT:GQ:DP	0/1:245:32	0/1:245:32
+1	3157410	.	GA	G	90.6	q10	AN=4;AC=4	GT:GQ:DP	1/1:21:21	1/1:21:21
+1	3162006	.	GAA	G	60.2	PASS	AN=4;AC=2	GT:GQ:DP	0/1:212:22	0/1:212:22
+1	3177144	.	G	T	45	PASS	AN=4;AC=2	GT:GQ:DP	0/0:150:30	1/1:150:30
+1	3177144	.	G	.	45	PASS	AN=4;AC=0	GT:GQ:DP	0/0:150:30	0/0:150:30
+1	3184885	.	TAAAA	TA,T	61.5	PASS	AN=4;AC=2,2	GT:GQ:DP	1/2:12:10	1/2:12:10
+2	3199812	.	G	GTT,GT	82.7	PASS	AN=4;AC=2,2	GT:GQ:DP	1/2:322:26	1/2:322:26
+3	3212016	.	CTT	C,CT	79	PASS	AN=4;AC=2,2	GT:GQ:DP	1/2:91:26	1/2:91:26
+4	3258448	.	TACACACAC	T	59.9	PASS	AN=4;AC=2	GT:GQ:DP	0/1:325:31	0/1:325:31
+4	4000000	.	T	A,C	59.9	PASS	AN=4;AC=2	GT:GQ:DP	0/1:325:31	0/1:325:31
+4	4000001	.	T	A	59.9	PASS	AN=4;AC=2	GT:GQ:DP	0/1:325:31	0/1:325:31