Changes

== Overview of Alignment Pipeline Steps ==  

== List of Alignment Sub-Pipelines ==  

The Alignment/Mapping Pipeline takes [http://en.wikipedia.org/wiki/FASTQ_format FASTQ files] and generates recalibrated [[BAM|BAM (Binary Sequence Alignment/Map format) files]] from them.  

 

 

This sub-pipeline takes in a list of bam files for each sample, merges the BAMs for samples that have multiple BAMs, dedups and recalibrates, and then indexes the recalibrated BAM.

 

 

This sub-pipeline does everything that *recab* does (takes in a list of bam files for each sample, merges the BAMs for samples that have multiple BAMs, dedups and recalibrates, and then indexes the recalibrated BAM). It then goes the next step to perform quality control (running qplot and verifyBamID).

 

 

This sub-pipeline takes in a single, recalibrated BAM file and its index file (.bai) and performs quality control (running qplot and verifyBamID). It differs from *bamQC_createIndex* in that it requires that the user already have .bai files for the recalibrated BAM files.

 

This sub-pipeline takes in a single, recalibrated BAM file, creates an index file for it, and performs quality control (running qplot and verifyBamID). It differs from *bamQC* in that it does not require that the user already have a .bai file for the recalibrated BAM file.

 

 

 

The automated test runs the alignment pipeline on a small set of test data and checks that the results against expected results validating that GotCloud is installed correctly.  

The automated test runs the alignment pipeline on a small set of test data and checks that the results against expected results validating that GotCloud is installed correctly.