bam2cram.smk¶
Snakemake workflow for file format conversion from BAM to CRAM to compress the file size.
Note
Please make sure that you have Singularity and Snakemake installed on your system and cloned the SnakeNgs repository.
Workflow¶
The rulegraph was created by snakevision.
Usage¶
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path/to/output
is the directory where the log files will be saved.path/to/reference_genome.fa
is the reference genome file in FASTA format (e.g.,Mus_musculus.GRCm38.dna_sm.primary_assembly.fa
for mouse genome).path/to/bam_list.txt
is a text file containing the list of BAM files to be converted to CRAM files:
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The CRAM files will be saved in the same directory as the input BAM files with the .cram
extension.