1##fileformat=VCFv4.1 2##INFO=<ID=TEST,Number=1,Type=Integer,Description="Testing Tag"> 3##FORMAT=<ID=TT,Number=A,Type=Integer,Description="Testing Tag, with commas and \"escapes\" and escaped escapes combined with \\\"quotes\\\\\""> 4##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases"> 5##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 6##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> 7##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> 8##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood"> 9##FILTER=<ID=q10,Description="Quality below 10"> 10##FILTER=<ID=test,Description="Testing filter"> 11##contig=<ID=1,assembly=b37,length=249250621> 12##contig=<ID=2,assembly=b37,length=249250621> 13##contig=<ID=3,assembly=b37,length=198022430> 14##contig=<ID=4,assembly=b37,length=191154276> 15##test=<ID=4,IE=5> 16##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta 17##readme=AAAAAA 18##readme=BBBBBB 19##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes"> 20##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> 21##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> 22##INFO=<ID=STR,Number=1,Type=String,Description="Test string type"> 23#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A B 241 3000150 . C T 59.2 PASS AN=4;AC=2 GT:GQ 0/1:245 0/1:245 251 3000151 . C T 59.2 PASS AN=4;AC=2 GT:DP:GQ 0/1:32:245 0/1:32:245 261 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,-20 271 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,-20 281 3106154 . CAAA C 342 PASS AN=4;AC=2 GT:GQ:DP 0/1:245:32 0/1:245:32 291 3106154 . C CT 59.2 PASS AN=4;AC=2 GT:GQ:DP 0/1:245:32 0/1:245:32 301 3157410 . GA G 90.6 q10 AN=4;AC=4 GT:GQ:DP 1/1:21:21 1/1:21:21 311 3162006 . GAA G 60.2 PASS AN=4;AC=2 GT:GQ:DP 0/1:212:22 0/1:212:22 321 3177144 . G T 45 PASS AN=4;AC=2 GT:GQ:DP 0/0:150:30 1/1:150:30 331 3177144 . G . 45 PASS AN=4;AC=0 GT:GQ:DP 0/0:150:30 0/0:150:30 341 3184885 . TAAAA TA,T 61.5 PASS AN=4;AC=2,2 GT:GQ:DP 1/2:12:10 1/2:12:10 352 3199812 . G GTT,GT 82.7 PASS AN=4;AC=2,2 GT:GQ:DP 1/2:322:26 1/2:322:26 363 3212016 . CTT C,CT 79 PASS AN=4;AC=2,2 GT:GQ:DP 1/2:91:26 1/2:91:26 374 3258448 . TACACACAC T 59.9 PASS AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31 384 4000000 . T A,C 59.9 PASS AN=4;AC=2,0 GT:GQ:DP 0/1:325:31 0/1:325:31 394 4000001 . T A 59.9 PASS AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31 40