annotate test-data/vcffixup-test1.vcf @ 2:fc5a64fdd5b2 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffixup commit c2af291b241e37e0a55adbc1fc72a9fa37d93582

##fileformat=VCFv4.0
##fileDate=20090805
##source=myImputationProgramV3.1
##reference=1000GenomesPilot-NCBI36
##phasing=partial
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
##FILTER=<ID=q10,Description="Quality below 10">
##FILTER=<ID=s50,Description="Less than 50% of samples have data">
##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=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
##ALT=<ID=DEL:ME:ALU,Description="Deletion of ALU element">
##ALT=<ID=CNV,Description="Copy number variable region">
##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">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
19	111	.	A	C	9.6	.	AC=1;AF=0.166667;AN=6;NS=3	GT:HQ	0|0:10,10	0|0:10,10	0/1:3,3
19	112	.	A	G	10	.	AC=1;AF=0.166667;AN=6;NS=3	GT:HQ	0|0:10,10	0|0:10,10	0/1:3,3
20	14370	rs6054257	G	A	29	PASS	AC=3;AF=0.5;AN=6;DP=14;NS=3;DB;H2	GT:GQ:DP:HQ	0|0:48:1:51,51	1|0:48:8:51,51	1/1:43:5:.,.
20	17330	.	T	A	3	q10	AC=1;AF=0.166667;AN=6;DP=11;NS=3	GT:GQ:DP:HQ	0|0:49:3:58,50	0|1:3:5:65,3	0/0:41:3:.,.
20	1110696	rs6040355	A	G,T	67	PASS	AA=T;AC=2,4;AF=0.333333,0.666667;AN=6;DP=10;NS=3;DB	GT:GQ:DP:HQ	1|2:21:6:23,27	2|1:2:0:18,2	2/2:35:4:.,.
20	1230237	.	T	.	47	PASS	AA=T;AC=0;AF=0;AN=6;DP=13;NS=3	GT:GQ:DP:HQ	0|0:54:.:56,60	0|0:48:4:51,51	0/0:61:2:.,.
20	1234567	microsat1	G	GA,GAC	50	PASS	AA=G;AC=3,1;AF=0.5,0.166667;AN=6;DP=9;NS=3	GT:GQ:DP	0/1:.:4	0/2:17:2	1/1:40:3
20	1235237	.	T	.	0	.	AC=0;AF=0;AN=4;NS=3	GT	0/0	0|0	./.
X	10	rsTest	AC	A,ATG	10	PASS	AC=1,1;AF=0.2,0.2;AN=5;NS=3	GT	0	0/1	0|2