Annovar produces uncalled mutations?

Question

[vctrm67]

I have a VCF of somatic calls produced by Mutect that I then annotated with Annovar. However, when I go to look up some of the mutations in the resulting output of Annovar, I can't find them in the original VCF that I inputted to Annovar. Why is this? Does Annovar have some margin of error for base location that it then annotates?

(base) $ grep "BRCA" vcf.hg19_multianno.txt 
chr13   32970929    32970929    T   -   intronic    BRCA2   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   0.25    .   87  chr13   32970928    .   CT  C   .   t_lod_fstar ECNT=1;HCNT=1;MAX_ED=.;MIN_ED=.;NLOD=26.10;RPA=6,5;RU=T;STR;TLOD=5.32   GT:AD:AF:ALT_F1R2:ALT_F2R1:QSS:REF_F1R2:REF_F2R1    0/1:55,4:0.068:1:3:1832,134:26:29   0/0:87,0:0.00:0:0:2827,0:37:50
chr17   41228491    41228491    T   G   intronic    BRCA1   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   0.25    .   289 chr17   41228491    .   T   G   .   PASS    ECNT=1;HCNT=1;MAX_ED=.;MIN_ED=.;NLOD=84.17;TLOD=123.44  GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1  0/1:137,42:0.239:22:20:0.524:4393,1454:65:72    0/0:289,0:0.00:0:0:.:9414,0:140:149
chr17   41242939    41242940    CA  -   intronic    BRCA1   .   .   .   rs138447886 0.0149  0.0142  0.0212  0.0260  0.0157  0.0165  0.0149  0.0052  0   0   0   0   0   0   0   0.25    .   447 chr17   41242938    .   GCA G   .   alt_allele_in_normal;str_contraction    ECNT=1;HCNT=6;MAX_ED=.;MIN_ED=.;NLOD=110.51;RPA=6,5;RU=CA;STR;TLOD=9.05 GT:AD:AF:ALT_F1R2:ALT_F2R1:QSS:REF_F1R2:REF_F2R1    0/1:338,7:0.021:3:4:11180,235:166:172   0/0:441,6:0.014:4:2:14845,208:224:217
chr17   41262498    41262498    G   A   intronic    BRCA1   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   0.25    .   72  chr17   41262498    .   G   A   .   t_lod_fstar ECNT=1;HCNT=6;MAX_ED=.;MIN_ED=.;NLOD=21.62;TLOD=4.16    GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1  0/1:51,2:0.038:1:1:0.500:1616,69:25:26  0/0:72,0:0.00:0:0:.:2400,0:29:43
(base) $ grep "32970929" vcf
(base) $

Answer 1

[Kevin Blighe]

If you run the following, you will find it:

grep "32970928" vcf

...and it should appear as something like:

chr13   32970928   .   CT   C

ANNOVAR expects indels to be in a specific format.

Kevin

[vctrm67]

I did that, as you can see, but it did not work. I was able to find some mutations this way, but could not find others.

[Kevin Blighe]

Are you sure? You did this:

grep "32970929" vcf

32970929 (you) versus 32970928 (me)