1. Community
2. Somatic
3. Why do a clear expected variant not show up in the Mutect2 vcf file

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 o...

• View comment
• Nabeel Ahmed
• April 29, 2021 22:53
• 0 votes

1. Community
2. Somatic
3. Why do a clear expected variant not show up in the Mutect2 vcf file

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...

• View comment
• Nabeel Ahmed
• April 10, 2021 00:36
• 0 votes

1. Community
2. Somatic
3. Why do a clear expected variant not show up in the Mutect2 vcf file

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...

• View comment
• Nabeel Ahmed
• April 08, 2021 20:07
• 0 votes

1. Community
2. Somatic
3. Why do a clear expected variant not show up in the Mutect2 vcf file

Yes. I have. There is no change in output.

• View comment
• Nabeel Ahmed
• April 07, 2021 18:31
• 0 votes

1. Community
2. Somatic
3. Why do a clear expected variant not show up in the Mutect2 vcf file

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 o...

• View comment
• Nabeel Ahmed
• April 07, 2021 16:46
• Edited
• 0 votes