8.4 VCF header

The first section of a VCF is a multi-line header – marked by the ## character – which contains metadata and descriptions of some of the columns (like INFO and FORMAT).

##fileformat=VCFv4.2
##fileDate=20200327
##source=PLINKv1.90
##contig=<ID=1,length=247169191>
##contig=<ID=2,length=242739671>
##contig=<ID=3,length=199318156>
##contig=<ID=4,length=191166588>
##contig=<ID=5,length=180617248>
##contig=<ID=6,length=170727838>
##contig=<ID=7,length=158798775>
##contig=<ID=8,length=146266471>
##contig=<ID=9,length=140174583>
##contig=<ID=10,length=135279752>
##contig=<ID=11,length=134426071>
##contig=<ID=12,length=132256834>
##contig=<ID=13,length=114114508>
##contig=<ID=14,length=106354055>
##contig=<ID=15,length=100209453>
##contig=<ID=16,length=88670345>
##contig=<ID=17,length=78634628>
##contig=<ID=18,length=76098044>
##contig=<ID=19,length=63771070>
##contig=<ID=20,length=62382908>
##contig=<ID=21,length=46924584>
##contig=<ID=22,length=49503800>
##INFO=<ID=PR,Number=0,Type=Flag,Description="Provisional reference allele, may not be based on real reference genome">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">

The final line of the header (marked with just one #) gives the names of the data columns. Note that there are over a hundred columns because each individual (1001, 1002, etc.) has their own column.

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  1001    1002    1003    1004    1005    1006    1007    1008    1009    1010    1011    1012    1013    1014    1015    1016    1017    1018    1019    1020    1021    1022    1023    1024    1025    1026    1027    1028    1029    1030    1031    1032    1033    1034
    1035    1036    1037    1038    1039    1040    1041    1042    1043    1044    1045    1046    1047    1048    1049    1050    1051    1052    1053    1054    1055
    1056    1057    1058    1059    1060    1061    1062    1063    1064    1065    1066    1067    1068    1069    1070    1071    1072    1073    1074    1075    1076
    1077    1078    1079    1080    1081    1082    1083    1084    1085    1086    1087    1088    1089    1090    1091    1092    1093    1094    1095    1096    1097
    1098    1099    1100    1101    1102    1103    1104    1105    1106    1107    1108    1109    1110    1111    1112    1113    1114    1115    1116    1117    1118
    1119    1120    1121    1122    1123    1124    1125    1126    1127    1128    1129    1130    1131    1132    1133    1134    1135    1136    1137    1138    1139
    1140    1141    1142    1143    1144    1145    1146    1147    1148    1149    1150    1151    1152    1153    1154    1155    1156    1157    1158    1159    1160
    1161    1162    1163    1164    1165    1166    1167    1168    1169    1170    1171    1172    1173    1174    1175    1176