SAMBLASTER: fast duplicate marking and structural variant read extraction.

ABSTRACT:

Motivation

Illumina DNA sequencing is now the predominant source of raw genomic data, and data volumes are growing rapidly. Bioinformatic analysis pipelines are having trouble keeping pace. A common bottleneck in such pipelines is the requirement to read, write, sort and compress large BAM files multiple times.

Results

We present SAMBLASTER, a tool that reduces the number of times such costly operations are performed. SAMBLASTER is designed to mark duplicates in read-sorted SAM files as a piped post-pass on DNA aligner output before it is compressed to BAM. In addition, it can simultaneously output into separate files the discordant read-pairs and/or split-read mappings used for structural variant calling. As an alignment post-pass, its own runtime overhead is negligible, wh

SUBMITTER: Faust GG 

PROVIDER: S-EPMC4147885 | biostudies-literature | 2014 Sep

REPOSITORIES: biostudies-literature