RemoveCramTags

What is this?

A program to quickly remove tag(s) from SAM/BAM/CRAM files

Install

RemoveCramTags relies on htslib. If you are using conda:

export CONDA_PREFIX=/path/to/miniconda3
make

If you have htslib in a directory somewhere:

export HTSLIB=/path/to/htslib
make

If you are using conda-build:

conda-build .
# change this to correct path:
conda install miniconda3/conda-bld/linux-64/remove-cram-tags-0.0.1-h2bc3f7f_0.tar.bz2

Otherwise set LDFLAGS and CPPFLAGS, e.g:

CPPFLAGS="-I/htslib" LDFLAGS+="-L/htslib" make

Usage

Run using:

Usage: RemoveCramTags [ARGS]

Positional arguments:

RemoveCramTags DThreads CThreads REF INPUT OUTPUT TAGS
    DThreads - Decompression threads
    CThreads - Compression threads
    REF      - Reference fasta file
    INPUT    - Input SAM/BAM/CRAM
    OUTPUT   - Output SAM/BAM/CRAM
    TAGS     - List of tags, comma separated

Example usage:

RemoveCramTags 4 2 $HG19 in.bam out.bam BI,BD

RemoveCramTags 4 2 $HG19 in.bam out.cram BI

RemoveCramTags 4 2 $HG19 - - BI   # stdin to stdout; output format will be cram