Search Results for "samtools"

Hadoop-BAM is a Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework with the Picard SAM JDK, and command line tools similar to SAMtools. The file formats currently supported are BAM, SAM, FASTQ, FASTA, QSEQ, BCF, and VCF. For a longer high-level description of Hadoop-BAM, refer to the article "Hadoop-BAM: directly manipulating next generation sequencing data in the cloud" in Bioinformatics Volume 28 Issue 6 pp. 876-877, available online at: http://dx.doi.org/10.1093/bioinformatics/bts054 Note that the library part of Hadoop-BAM is mainly for developers with experience in using Hadoop. ...

BCP is a command-line tool ideated to analyze NGS data, also offering a wrapper for some common NGS software, including Fastx and Samtools. It is oriented mainly towards targeted resequencing experiments, with a set of functions for general purposes. BCP also includes a function for breast cancer risk estimation, based on the Gail model, using both clinical and genome data.