Nabeel Ahmed
- Total activity 8
- Last activity
- Member since
- Following 0 users
- Followed by 0 users
- Votes 1
- Subscriptions 1
Activity overview
Latest activity by Nabeel Ahmed-
Nabeel Ahmed commented,
Hi Genevieve-Brandt-she-her, Thank you for taking a look into this. I followed your recommendation of lowering the --pruning-lod-threshold but this call is still unable to make it to the output of ...
-
Nabeel Ahmed commented,
Thank you for digging into this. I have followed the instructions and have uploaded a tar.gz with the name mutect2_nabeel_somatic_query_data_v2.tar.gz containing the dot files, log, input bam and o...
-
Nabeel Ahmed commented,
Giving an update. I tried Mutect2 in a previous version of GATK 4.1.3.0 and I am seeing the expected call that is being missed above.The following is the call in the vcf output from Mutect2 chr12 2...
-
Nabeel Ahmed commented,
Yes. I have. There is no change in output.
-
Nabeel Ahmed commented,
Thanks for your reply Genevieve-Brandt-she-her. I am sorry for the confusion. I am showing two different sections of the log for comparison of two expected calls (one which is detected and the oth...
-
Nabeel Ahmed created a post,
Why do a clear expected variant not show up in the Mutect2 vcf file
AnsweredI am running Mutect2 on a sample in tumor-only mode. This sample has mutations introduced and known to be true positive calls. However, I am unable to detect some of these calls in the vcf file aft...