Presence of unknown sites in ANNOVAR output file

Question

[sainavyav22]

Hello,

I am using ANNOVAR to annotate my dog tumor Illumina whole genome sequenced DNA reads. It generated 3 output files:

1. exonic.variant.function
2. variant_function; and
3. .log

My exonic variant function file has many unknown sites. Is this common?

line1869        unknown UNKNOWN NC_006583.3     78409995        78409995        C       T       het     .       268
     93
line1870        unknown UNKNOWN NC_006583.3     78410043        78410043        T       C       het     .       252
     93
line2130        frameshift deletion     gene-PTAR1:XM_022421328.1:exon3:c.49delT:p.F17fs,gene-PTAR1:XM_022421312.1:exon3:c.49delT:p.F17fs,gene-PTAR1:XM_022421323.1:exon3:c.49delT:p.F17fs,gene-PTAR1:XM_022421320.1:exon6:c.49delT:p.F17fs,gene-PTAR1:XM_022421302.1:exon6:c.49delT:p.F17fs,gene-PTAR1:XM_022421307.1:exon4:c.49delT:p.F17fs,  NC_006583.3     87686229        87686229        T       -       het     .       174
line2485        nonsynonymous SNV       gene-LOC100685225:XM_014114614.2:exon3:c.G1447A:p.E483K,        NC_006583.3
     100461847       100461847       C       T       het     .       262     93

Someone please help me with this. Thanks

[Ram]

Please show us your full annovar command line.

[sainavyav22]

Here you go.

perl convert2annovar.pl -format vcf4old 1008_Tumor.vcf > 1008Tumor_variant.avinput
perl annotate_variation.pl 1008Tumor_variant.avinput dogdb/ -buildver dog -out AnnotatedOutput/1008Tumor