BamUtil and libStatGen

bamUtil is a repository that contains several programs that perform operations on SAM/BAM files. All of these programs are built into a single executable, bam.

libStatGen

Full documentation

http://genome.sph.umich.edu/wiki/BamUtil
http://genome.sph.umich.edu/wiki/C%2B%2B_Library:_libStatGen

Git

https://github.com/statgen/bamUtil

Build Docker image

sudo docker build -t compbio/ngseasy-bamtuil .

Get Docker image

sudo docker pull compbio/ngseasy-bamtuil:latest

Run Docker image

  • http://genome.sph.umich.edu/wiki/BamUtil:_recab
sudo docker run -i -t compbio/ngseasy-bamtuil /usr/local/pipeline/bamUtil/bin/bam recab --in ${INPUT}.bam --out ${OUTPUT}.bam --refFile ${REF} --dbsnp ${DBSNP} --storeQualTag OQ --maxBaseQual 40