BAM preprocessing
Dump normal pairs into a file sample_name.norm.bam/sam

What it does

Bam_preprocessingPairs - Version 0.5

Preprocessing of mates to get anomalously mapped mate-pair/paired-end reads as input for SVDetect.

From all pairs mapped onto the reference genome, this script outputs abnormal pairs:

  • mapped on two different chromosomes
  • with an incorrect strand orientation and/or pair order
  • with an insert size distance +- sigma threshold

into a file prefix.ab.bam/sam sorted by read names

-BAM/SAM File input format only.

SAMtools required for BAM files

Contact Bruno Zeitouni ( for any questions or concerns about the Galaxy implementation of SVDetect.