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Good afternoon, I am working with GATK 4.1.7.0 and am attempting to use the CollectAllelicCounts function as part of a somatic CNV Workflow.  I need some additional help with the interval list that...

• jejacobs23
• May 18, 2020 22:33
• 8 followers
• 15 comments
• 1 vote

1. Community
2. Somatic

I am using the Copy Number Variation (CNV) tutorial in order to analyze whole genome sequencing samples (along with matched normal controls).  When I run the GATK tool, CollectAllelicCounts, I get ...

• jejacobs23
• August 18, 2020 22:52
• 4 followers
• 14 comments
• 0 votes

1. Community
2. Somatic

Hello, I'm using the took CollectAllelicCounts with GATK version 4.1.7.0 and I'm having difficulty with the output file.  My code is as follows: REF=<path_to_directory>"/Homo_sapiens_assembly38.fas...

• jejacobs23
• August 04, 2020 22:01
• 2 followers
• 1 comment
• 0 votes

1. Community
2. Other

With the update in the website, I can no longer find the documentation for GATK3.  Did that move to a different location?

• jejacobs23
• February 24, 2020 20:20
• 2 followers
• 1 comment
• 0 votes