Ren Hamm
- Total activity 9
- Last activity
- Member since
- Following 0 users
- Followed by 0 users
- Votes 0
- Subscriptions 2
Activity overview
Latest activity by Ren Hamm-
Ren Hamm commented,
##fileformat=VCFv4.2##ALT=<ID=NON_REF,Description="Represents any possible alternative allele not already represented at this location by REF and ALT">##FORMAT=<ID=AD,Number=R,Type=Integer,Descript...
-
Ren Hamm commented,
Thank you! I'm getting a strange error now, though. I am running this command: /global/scratch/users/laurenhamm/thesis/aim2/vcfs/gatk_reinstall/gatk-4.6.1.0/gatk --java-options "-Xmx64G" GenotypeGV...
-
Ren Hamm commented,
Redownloading the newest version seemed to fix the original issue, and I can successfully make Mutect2 mitocondrial mode vcfs that then can be filtered. However, I need to get allele frequency data...
-
Ren Hamm commented,
Of course! This DNA data is from WGS 150bp paired-end Illumina reads, which were aligned using BWA-mem.
-
Ren Hamm commented,
I ran everything again after removing all the additional filter parameters, and I am still recieving the same error.
-
Ren Hamm created a post,
Mutect2 Calls for non-tumor pooled samples - no variants pass filters
I am using Mutect2 as suggested to variant call non-tumor samples consisting of multiple individuals that were pooled together and sequenced as one. This affects the ploidy value. However, FilterMu...
-
Ren Hamm commented,
I am receiving the same error using GATK version 4.4.0. Has there been any resolution to this issue?