If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
The ComputeGenomeMaskStatistics utility prints the number of alignable and unalignable bases.
2. Inputs / Arguments
-I <mask-file>: The genome mask file. An indexed fasta file containing
the genome mask. The fasta file must be indexed with
samtools faidxor the
-R <fasta-file>: Reference sequence. An indexed fasta file containing
the reference sequence to mask. The fasta file must be indexed with
samtools faidxor the equivalent.
-O <mask-file>: Tab-delimited output file containing the number of
alignable and unalignable bases (per chromosome and total). Default is to