merge
Category: ALIGNMENT
Merge pre-sorted BAM files into a single sorted BAM
Description
Merge pre-sorted BAM files into a single sorted BAM.
Performs a k-way merge of multiple BAM files that are already sorted in the
same order, producing a single merged output that preserves the sort order.
Similar to samtools merge, but supports template-coordinate order.
Input files must all be sorted in the specified sort order.
EXAMPLES:
Merge coordinate-sorted BAMs
fgumi merge -o merged.bam sorted1.bam sorted2.bam sorted3.bam
Merge template-coordinate sorted BAMs
fgumi merge -o merged.bam –order template-coordinate tc1.bam tc2.bam
Merge from a file listing input BAMs (one per line)
fgumi merge -o merged.bam -b input_list.txt –order queryname
Merge with multiple threads
fgumi merge -o merged.bam -@ 4 sorted1.bam sorted2.bam
Arguments
| Flag | Description | Default |
|---|---|---|
-o, --output <OUTPUT> | Output BAM file | required |
inputs <INPUTS> | Input BAM files to merge (positional) | |
-b, --input-list <INPUT_LIST> | File containing a list of input BAM paths, one per line | |
--order <ORDER> | Sort order of the input files | template-coordinate |
-@, --threads <THREADS> | Number of threads for parallel operations | 1 |
--compression-level <COMPRESSION_LEVEL> | Compression level for output BAM (1-12) | 6 |