Samtools trio calling (DNAnexus Platform App)

Trio calling (with recognition of mendelian violations) using samtools from https://github.com/samtools/samtools/archive/0.1.19.tar.gz

This is the source code for an app that runs on the DNAnexus Platform. For more information about how to run or modify it, see https://wiki.dnanexus.com/.

Caveat:

This applet does not properly handle non-pseudoautosomal regions of the X chromosome correctly.

getting/building the source

The git repo needs to be checked out with git clone --recursive to get the samtools source.

If you did not do this and already have the source, try git submodule init then git submodule update

To build, you need the DNANexus SDK installed, then issue dx build from within this directory.

Inputs

• Input BAM file for child childbam: file
• Input BAM file for the father fatherbam: file
• Input BAM file for the mother motherbam: file

The input BAM files need to have an appropriate SAMPLE_NAME property which will be used in the output VCF

• Reference genome reference: file
• File containing target regions (.bed) targetbed: file (optional)

Outputs

• Joint calls with trio MV calculations vcfout: file