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merge.abc.2.out
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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>
##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">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=TXT,Number=.,Type=String,Description="Testing in INFO">
##INFO=<ID=XRF,Number=R,Type=Float,Description="Test Number=AGR in INFO">
##INFO=<ID=XAF,Number=A,Type=Float,Description="Test Number=AGR in INFO">
##INFO=<ID=XGF,Number=G,Type=Float,Description="Test Number=AGR in INFO">
##INFO=<ID=XRI,Number=R,Type=Integer,Description="Test Number=AGR in INFO">
##INFO=<ID=XAI,Number=A,Type=Integer,Description="Test Number=AGR in INFO">
##INFO=<ID=XGI,Number=G,Type=Integer,Description="Test Number=AGR in INFO">
##INFO=<ID=XRS,Number=R,Type=String,Description="Test Number=AGR in INFO">
##INFO=<ID=XAS,Number=A,Type=String,Description="Test Number=AGR in INFO">
##INFO=<ID=XGS,Number=G,Type=String,Description="Test Number=AGR in INFO">
##SAMPLE=<ID=NORMAL,SampleName=B,Description="Less-than (\"<\") and greater-than (\">\") quoting nonsense where double brackets would do just fine",softwareName=<Nonsense,Software>,softwareVer=<119,65>,softwareParam=<.>,MetadataResource=http://somewhere.com/path>
##FORMAT=<ID=STR,Number=1,Type=String,Description="Testing string in format">
##FILTER=<ID=q20,Description="Mapping quality below 20">
##INFO=<ID=INTA,Number=A,Type=Integer,Description="Testing Number=A in INFO">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A B 2:B C D
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 84.6 q10;q20 INDEL;STR=test;TXT=AA;DP=1013;DP4=6,7,8,9;AN=10;AC=5 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20 0/1:409:35:-20,-5,-20 0/1:376:14:-10,0,-10 0/1:409:35:-20,-5,-20 0/1:409:35:-20,-5,-20
1 3062915 idSNP G T,C,A 419 test;q20 TEST=5;STR=.;DP=14;DP4=3,6,9,12;INTA=2,1,.;AN=9;AC=2,2,1 GT:TT:GQ:DP:GL:STR 0/1:0,1,.:409:35:-20,-5,-20,-20,-5,-20,.,.,.,.:. 2:0,1,.:409:35:-20,-5,-20,.:. 0/3:.:376:14:-10,.,.,.,.,.,0,.,.,-10:ABC 0/2:1,0,.:409:35:-20,-20,-20,-5,-5,-20,.,.,.,.:. 0/1:1,0,.:409:35:-20,-20,-20,-5,-5,-20,.,.,.,.:.
1 3062915 id1D;id2D GTT GT,G 999 q20;q10 DP=14;DP4=2,4,6,8;AN=6;AC=1,2 GT:GQ:DP:GL:STR ./.:.:.:.:. ./.:.:.:.:. 0/1:376:14:-10,0,-10,.,.,.:DEF 0/2:409:35:-20,.,.,-5,.,-20:. 0/2:409:35:-20,.,.,-5,.,-20:.
1 3106154 . CAAAA CA,C 342 PASS DP=15;AN=6;AC=2,1 GT:GQ:DP:GL 0/1:245:32:. 0/1:245:32:. 0/2:277:15:-10,.,.,0,.,-10 .:245:32:. ./.:245:32:.
1 3106154 . C CT 459 PASS AN=8;AC=4 GT:GQ:DP 0/1:245:32 0/1:245:32 ./.:.:. 0/1:245:32 0/1:245:32
1 3106154 . C T 999 PASS DP=15;AN=2;AC=1 GT:GQ:DP:GL ./.:.:.:. ./.:.:.:. 0/1:277:15:-10,0,-10 ./.:.:.:. ./.:.:.:.
1 3157410 . GAC GC,G 90.6 PASS DP=11;AN=6;AC=4,1 GT:GQ:DP 1/1:21:21 1/1:21:21 0/2:49:11 ./.:.:. ./.:.:.
1 3157410 . G T 46.7 q10 AN=4;AC=4 GT:GQ:DP ./.:.:. ./.:.:. ./.:.:. 1/1:21:21 1/1:21:21
1 3162006 . GAA G,GA 238 PASS DP=19;XRF=1e+06,2e+06,500000;XRI=1111,2222,5555;XRS=AAA,BBB,DDD;XAF=1e+06,500000;XAI=1111,5555;XAS=AAA,DDD;XGF=1e+06,2e+06,3e+06,500000,.,9e+09;XGI=1111,2222,3333,5555,.,9999;XGS=A,B,C,E,.,F;AN=10;AC=3,2 GT:GQ:DP 0/1:212:22 0/1:212:22 0/1:589:19 0/2:212:22 0/2:212:22
1 3177144 . G T 999 PASS DP=24;AN=10;AC=3 GT:GQ:DP 0/0:150:30 1/1:150:30 0/1:236:24 0/0:150:30 0/0:150:30
1 3177144 . GT G 999 PASS DP=24;AN=6;AC=1 GT:GQ:DP 0/0:150:30 0/0:150:30 0/1:236:24 ./.:.:. ./.:.:.
1 3184885 . TAAAA TA,T 61.5 PASS DP=16;AN=10;AC=5,4 GT:GQ:DP 1/2:12:10 1/2:12:10 0/1:435:16 1/2:12:10 1/2:12:10
2 3188209 . GA G 41.5 PASS DP=15;AN=2;AC=1 GT:GQ:DP ./.:.:. ./.:.:. 0/1:162:15 ./.:.:. ./.:.:.
2 3199812 . G GTT,GT 291 PASS AN=8;AC=4,4 GT:GQ:DP 1/2:322:26 1/2:322:26 ./.:.:. 1/2:322:26 1/2:322:26
3 3199812 . GA GTT,GT 17.5 PASS DP=19;AN=2;AC=1,1 GT:GQ:DP ./.:.:. ./.:.:. 1/2:188:19 ./.:.:. ./.:.:.
3 3212016 . CTT C,CT 79 PASS AN=8;AC=4,4 GT:GQ:DP 1/2:91:26 1/2:91:26 ./.:.:. 1/2:91:26 1/2:91:26
4 3212016 . CTT C 999 q20 DP=15;AN=2;AC=1 GT:GQ:DP ./.:.:. ./.:.:. 0/1:158:15 ./.:.:. ./.:.:.
4 3258448 . TACACACAC T . PASS AN=8;AC=4 GT:GQ:DP 0/1:325:31 0/1:325:31 ./.:.:. 0/1:325:31 0/1:325:31