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##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,-20,-5,-20 2|2:0,1:409:35:-20,-5,-20,-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
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