Annovar produces uncalled mutations?
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18 months ago
vctrm67 ▴ 20

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) \$

annovar • 315 views
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18 months ago

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

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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.

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Are you sure? You did this:

grep "32970929" vcf


32970929 (you) versus 32970928 (me)