Hello,

I tried to perform variant annotation using Annovar. I created a bed file containing regions of interest, and followed the instructions on their webpage. Their example was:

[kaiwang@biocluster ~/]$ annotate_variation.pl ex1.hg18.avinput humandb/ -bedfile hg18_SureSelect_All_Exon_G3362_with_names.bed -dbtype bed -regionanno -out ex1

NOTICE: The --buildver is set as 'hg18' by default
NOTICE: Reading annotation database hg18_SureSelect_All_Exon_G3362_with_names.bed ... Done with 165637 regions
NOTICE: Finished region-based annotation on 12 genetic variants in ex1.human NOTICE: Output files were written to ex1.hg18_bed

[kaiwang@biocluster ~/]$ cat ex1.hg18_bed

bed Name=NA 1 67478546 67478546 G A comments: rs11209026 (R381Q), a SNP in IL23R associated with Crohn's disease
bed Name=NA 2 233848107 233848107 A G comments: rs2241880 (T300A), a SNP in the ATG16L1 associated with Crohn's disease
bed Name=NA 16 49303427 49303427 C T comments: rs2066844 (R702W), a non-synonymous SNP in NOD2
bed Name=NA 16 49314041 49314041 G C comments: rs2066845 (G908R), a non-synonymous SNP in NOD2

My command was:

perl annotate_variation.pl final.avinput galGal4db/ -bedfile GoIBED.bed -dbtype bed -regionanno -out mpileup --buildver galGal4

And here is a sample of my output:

bed    Name=NA    1    6559588    6559588    C    G    1    228    51    1    6559588    .    C    G    228    PASS    AC=2;AN=2;DP=51;DP4=0,0,25,23;MQ=60;MQ0F=0;MQSB=1;SGB=-0.693147;VDB=0.302532    GT:PL:GQ    1/1:255,144,0:127<br />
bed    Name=NA    1    6559683    6559683    T    C    0.5    183    50    1    6559683    .    T    C    183    PASS    AC=1;AN=2;BQB=0.350305;DP=50;DP4=11,11,14,12;HOB=0.5;ICB=1;MQ=60;MQ0F=0;MQB=1;MQSB=1;RPB=0.961737;SGB=-0.692976;VDB=0.98812    GT:PL:GQ    0/1:216,0,205:127<br />
bed    Name=NA    1    6559756    6559756    A    G    0.5    179    53    1    6559756    .    A    G    179    PASS    AC=1;AN=2;BQB=3.34386e-05;DP=53;DP4=16,8,13,12;HOB=0.5;ICB=1;MQ=60;MQ0F=0;MQB=1;MQSB=1;RPB=0.359713;SGB=-0.692914;VDB=0.042852    GT:PL:GQ    0/1:212,0,207:127<br />
bed    Name=NA    1    6559924    6559924    G    A    0.5    161    60    1    6559924    .    G    A    161    PASS    AC=1;AN=2;BQB=0.0112166;DP=60;DP4=15,12,16,12;HOB=0.5;ICB=1;MQ=60;MQ0F=0;MQB=1;MQSB=1;RPB=0.988586;SGB=-0.693054;VDB=0.469081    GT:PL:GQ    0/1:194,0,208:127<br />
bed    Name=NA    1    6559988    6559988    A    G    0.5    137    57    1    6559988    .    A    G    137    PASS    AC=1;AN=2;BQB=9.15355e-05;DP=57;DP4=14,15,11,16;HOB=0.5;ICB=1;MQ=60;MQ0F=0;MQB=1;MQSB=1;RPB=0.626272;SGB=-0.693021;VDB=0.298808    GT:PL:GQ    0/1:170,0,195:127

I checked the avinput file and noticed that the output is no different from my avinput file except it filtered the variants according to the regions I provided in the bed file, and added the first two columns (bed and Name=NA). Does anyone have any idea regarding what I should do to get proper annotations? I have also attached a portion of my avinput file for anyone interested. Thanks!

1       2264    2264    T       C       1       211     69      1       2264    .       T       C       211     PASS    AC=2;AN=2;DP=69;DP4=0,0,9,53;MQ=42;MQ0F=0;MQSB=0.475715;SGB=-0.693147;VDB=0.0254827     GT:PL:GQ        1/1:238,187,0:127<br />
1       2272    2272    A       T       1       189     71      1       2272    .       A       T       189     PASS    AC=2;AN=2;BQB=0.891667;DP=71;DP4=0,2,7,53;MQ=41;MQ0F=0;MQB=0.491667;MQSB=0.877341;RPB=0.716667;SGB=-0.693147;VDB=0.0635911      GT:PL:GQ        1/1:216,134,0:127<br />
1       9050    9050    A       G       1       228     50      1       9050    .       A       G       228     PASS    AC=2;AN=2;DP=50;DP4=0,0,28,19;MQ=45;MQ0F=0.02;MQSB=0.271417;SGB=-0.693147;VDB=0.0797358 GT:PL:GQ        1/1:255,141,0:127<br />
1       14689   14692   TCTG    -       0.5     218     34      1       14684   .       CTCTGTCTG       CTCTG   218     PASS    AC=1;AN=2;DP=34;DP4=0,5,7,15;HOB=0.5;ICB=1;IDV=25;IMF=0.735294;INDEL;MQ=44;MQ0F=0;MQSB=0.906686;SGB=-0.692562;VDB=0.877997      GT:PL:GQ        0/1:255,0,28:21