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 (email@example.com) for any questions or concerns about the Galaxy implementation of SVDetect.