Galaxy |

BAM preprocessing (version 1.0.0)

Sample Name:

BAM input file:

Read type:

Library type:

Do you want an additional bam file listing concordant mapped pairs?:

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

Number of pairs for calculating mu (µ) and sigma (σ) lengths:

Minimum value of ISIZE for calculating mu (µ) and sigma (σ) lengths:

Maximum value of ISIZE for calculating mu (µ)and sigma( σ) lengths:

Minimal number of sigma (σ) fold for filtering pairs:

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 (svdetect@curie.fr) for any questions or concerns about the Galaxy implementation of SVDetect.