Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

ComputeGenomeMaskStatistics

Geraldine_VdAuweraGeraldine_VdAuwera Posts: 5,692Administrator, GATK Developer admin
edited September 2012 in GenomeSTRiP Documentation

1. Introduction

The ComputeGenomeMaskStatistics utility prints the number of alignable and unalignable bases.

See ComputeGenomeMask.

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 faidx or the
    equivalent.

  • -R <fasta-file> : Reference sequence. An indexed fasta file containing
    the reference sequence to mask. The fasta file must be indexed with
    samtools faidx or the equivalent.

3. Outputs

  • -O <mask-file> : Tab-delimited output file containing the number of
    alignable and unalignable bases (per chromosome and total). Default is to
    write to stdout.
Post edited by Geraldine_VdAuwera on

Geraldine Van der Auwera, PhD

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