How to specify --colsWanted in annovar filter-based annotation?
0
0
Entering edit mode
7.4 years ago
jonessara770 ▴ 240

Hello,

I am trying to annotate my list of variants with hg19_icgc21.txt with annovar. The database looks like this:

MT 16326 16326 A G MU17729789 PACA-AU|1|391|0.00256 MT 16337 16337 C T MU16089244 OV-AU|1|93|0.01075 MT 16352 16352 T C MU29386732 PAEN-IT|1|37|0.02703 MT 16360 16360 C T MU13637878 OV-AU|1|93|0.01075 MT 16365 16365 C T MU22658014 RECA-EU|1|95|0.01053 MT 16366 16366 C T MU8784685 PACA-AU|1|391|0.00256

After running annovar , it outputs only column 6. What I want is column 6 and 7. I had a look at the software help but it seems --colsWanted works only for region-based annotation. Is there any other options that I can put to get column 7?

thanks

DNA-seq • 1.2k views
ADD COMMENT

Login before adding your answer.

Traffic: 1406 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6