---
name: "sga-bam2de"
section: "1"
platform: "linux"
package: "sga"
version: "0.10.15-7+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/sga-bam2de"
---

# sga-bam2de(1)

Make a distance estimate file from a bam file of reads aligned to contigs

## NAME

sga-bam2de - Make a distance estimate file from a bam file of reads aligned to contigs

## DESCRIPTION

sga-bam2de.pl - Make a distance estimate file from a bam file of reads aligned to contigs sga-bam2de.pl **-n** N **--prefix** lib300 lib300.bam Options:

- **-n** N

  Minimum number of pairs required to consider two contigs linked

- **-m** LEN

  Only find links between contigs with length at least LEN bp (default: 200)

- **-t** NUM

  Use NUM threads for computing the distance estimates

- **--prefix** NAME

  Use NAME as the prefix for the outfiles

- **--mind** D

  Set the minimum distance estimate to test to be D. This should be a negative number if contigs are expected to overlap. Defaults to **-99bp**.

- **--mina** N

  Set the minimum alignment length to be N.

- **--help**

  This help output.