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