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split_paired_bam.py

Split a paired-end BAM file into two single-end BAM files.

Usage

split_paired_bam.py -i input.bam -o output_prefix

Options

Option Description Default
-i, --input-file Alignment file in BAM or SAM format (sorted, indexed) Required
-o, --out-prefix Prefix of output BAM files Required

Output

  • prefix.R1.bam — first reads (read 1)
  • prefix.R2.bam — second reads (read 2)