Leo
- Total activity 12
- Last activity
- Member since
- Following 0 users
- Followed by 0 users
- Votes 3
- Subscriptions 4
Activity overview
Latest activity by Leo-
Leo created a post,
Mutect2 tumor-only mode without normal match or germline resources
Hi, If I use Mutect2 in tumor-only mode to call somatic variants without any normal match, panel of normals (PON) or other germline resources. Will the results contain many germline variants? Will ...
-
Leo created a post,
How number of somatic variants in the sample affects Mutect2 results?
Hi, I am calling somatic variants from an artificial cell mixture using Mutect2. The sample contains many more somatic variants than somatic mutation events in human tissue. Will Mutect2 (Calling, ...
-
Leo commented,
I am trying to calculate the indel events and use PF_INDEL_RATE * PF_ALIGNED_BASES / 100 based on the documentation. But the results are not integer.
-
Leo created a post,
Defination of PF_ALIGNED_BASES and PF_INDEL_RATE
Hi, I am using Picard (2.9.0) CollectAlignmentSummaryMetrics. May I ask how PF_ALIGNED_BASES is counted? Does it include both match and mismatched bases and exclude all indels, gaps and soft/hard ...
-
Leo created a post,
GenomicsDBImport: An index is required, but none found with file ending .idx
REQUIRED for all errors and issues: a) GATK version used: v4.4.0.0b) Exact command used: /gatk/gatk GenomicsDBImport --java-options "-Xmx160G -Xms160G" -R "${REF}" -L "${BED}" --merge-input-interv...