##fileformat=VCFv4.1
##FILTER=<ID=PASS,Description="All filters passed">
##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=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
##INFO=<ID=STR,Number=1,Type=String,Description="Test string type">
##bcftools_pluginCommand=plugin missing2ref -o test.out.vcf -- missing2ref -p -m
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A	B	C	D
1	3000150	.	C	T	59.2	PASS	.	GT:GQ	1|1:245	1|1:245	0/1:245	1/1:245
1	3000151	.	C	T	59.2	PASS	.	GT:DP:GQ	0|0:32:245	0|0:32:245	0|0:32:245	0|0:32:245
1	3062915	id3D	GTTT	G	12.9	q10	DP4=1,2,3,4;INDEL;STR=test	GT:GQ:DP:GL	0/1:409:35:-20,-5,-20	0/1:409:35:-20,-5,-20	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	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	2/2:0,1:409:35:-20,-5,-20	2|2:0,1:409:35:-20,-5,-20
2	3199812	.	G	GTT,GT	82.7	PASS	.	GT:GQ:DP	0|0:322:26	0|0:322:26	0|0:322:26	0|0:322:26
3	3212016	.	CTT	C,CT	79	PASS	.	GT:GQ:DP	0|0:91:26	0|0:91:26	0|0:91:26	0|0:91:26
4	3258448	.	TACACACAC	T	59.9	PASS	.	GT:GQ:DP	0|0:325:31	0|0:325:31	0|0:325:31	0|0:325:31