1. Community
2. Special GATK Use Cases
3. Mutect2 calls germline variants not present in germline resource

Thank you very much for the help Gökalp Çelik

• View comment
• Jaime Alvarez Benayas
• August 02, 2024 13:44
• 0 votes

1. Community
2. Special GATK Use Cases
3. Mutect2 calls germline variants not present in germline resource

Thank you Gökalp Çelik it does help a lot. What about the opposite case? Variants filtered as "germline" but not found in the germline population frequency resource. I am assuming this is because t...

• View comment
• Jaime Alvarez Benayas
• August 02, 2024 11:19
• 0 votes

1. Community
2. Special GATK Use Cases
3. Mutect2 - using a primary tumour sample instead of a normal sample

Hi Thomas Bradley, I am doing a similar kind of analysis as what you described (pseudonormal = tumor state 1, tumor = tumor state 2). Did you manage to run successfully the analysis you were descri...

• View comment
• Jaime Alvarez Benayas
• July 30, 2024 13:48
• 0 votes

1. Community
2. Somatic
3. Mutect2 using a tumor as "pseudonormal" and relapsed as "tumor", PON necessary?

Thank you, it did help!

• View comment
• Jaime Alvarez Benayas
• June 26, 2024 16:39
• 0 votes