User-Provided BAM Files

SaVor supports using your own BAM files instead of generating them from FASTQ files. To use this feature:

1. Add two new columns to your sample sheet (samples.csv):

   • bamPath: Full path to your BAM file

   • baiPath: Full path to your BAI file (index)

Example sample sheet with user-provided BAM files:

Run,BioSample,LibraryName,refGenome,refPath,bamPath,baiPath
SRR1945442,SAMN03326286,SAMN03326286,GCF_000001735.3,REFERENCE/TAIR10_REF.fna,/path/to/your/sample1.bam,/path/to/your/sample1.bam.bai
SRR1945443,SAMN03326287,SAMN03326287,GCF_000001735.3,REFERENCE/TAIR10_REF.fna,/path/to/your/sample2.bam,/path/to/your/sample2.bam.bai

When user-provided BAM files are detected, the workflow will:

1. Skip the FASTQ download/ingestion steps

2. Skip the read alignment steps

3. Copy your BAM files to the workflow’s expected location (results/{refGenome}/bams/{sample}_final.bam)

4. Use these copied BAM files for SV calling

Note:

• Ensure your BAM files are properly sorted and indexed.

• The workflow will copy your BAM files to maintain a consistent structure for downstream steps.

• You can mix samples with user-provided BAMs and samples that need alignment in the same run.

• The mark_duplicates setting is ignored for user-provided BAMs, as they are used as-is. Ensure BAM files provided to the workflow are properly marked for duplicates. One can do this with sambamba for example:

 sambamba markdup -t 8 -p input.bam output.bam

• The workflow performs file existence and permission checks at the time of use, providing clear error messages if files are missing or unreadable.

• Logs for user-provided BAM file operations are saved in logs/{refGenome}/user_bams/.