Genomics

Sort it, index it,and count what mapped

The common path over a SAM, BAM or CRAM file.Sorted, indexed and summarized, into output.

SAMtools 1.194 cores · 4 GBRuns as a job

hub://samtools

$ dxflow workflow create --identity samtools hub://samtools

$ dxflow workflow start samtools --override env.job.THREADS=8

01Pick a machinecores, memory and a rate per hour

02Create the workflowpulled from the hub, once

03Run it, then stopstopped when the work is done

The application

Three steps,and one job

Sort, index and flagstat, over whatever INPUT is pointing at.

Any of three formats

SAM, BAM or CRAM — samtools works out the format on its own here.

Sorted and indexed

sorted.bam and its .bai, ready for whatever needs to seek in one.

And counted

flagstat.txt: the totals, the mapped, the paired, the duplicates.

The job

A job, not a session — it ends once the three files are written.

inputInputyour alignment, read-only

outputOutputsorted, indexed, counted

Point INPUT at itThe default is /data/input/sample.sam — override it per run.

Watch it from the CLIdxflow workflow logs follows the run, and list shows the state.

Run SAMtools on your own machinePick a machine that meets it, and it opens about a minute after you ask.