View source for Tutorial: EMMAX GotCloud STOM: Lecture 5

STOM 2014 Workshop - Practical Sessions 5

== Lecture 5 ==

The slides describing the notes below are available [[Media:Stom practice 05.pdf | here (PDF)]]

=== Basic Setup ===

* To see the files for the session 5(,6, and 8), type

 ls /data/stom2014/session5/

If you see any errors, please let me know now!

* For convenience, let’s set some variables
 export S5=/data/stom2014/session5

* Also, let's relocate the output directory from the yesterday's class
 mv ~/out ~/out_session2

* And create a new output directory
 mkdir ~/out

* And check the input files
 ls $S5/examples/

=== Preparing Input Files ===

* Index file - See the example index file already prepared for this project

 cat $S5/examples/index/chr7.CFTR.fastq.index

* Configuration File - See the example configuration file below.
 cat $S5/examples/index/chr7.CFTR.align.conf
 
 INDEX_FILE = index/chr7.CFTR.fastq.index
 ###################
 # References
 REF_DIR = chr7Ref
 AS = NCBI37
 REF = $(REF_DIR)/hs37d5.chr7.fa
 DBSNP_VCF =  $(REF_DIR)/dbsnp_135.b37.chr7.CFTR.vcf.gz
 HM3_VCF = $(REF_DIR)/hapmap_3.3.b37.sites.chr7.CFTR.vcf.gz

Default options should be mostly fine in many other cases. In this example, because it is not genome-wide calling, reference files are modified to be chr7-specific

=== Run GotCloud Alignment Pipeline ===

* Using the prepared input files, align the FASTQ files using the gotcloud alignment pipeline

 $S5/gotcloud/gotcloud align --conf $S5/examples/index/chr7.CFTR.align.conf  --outDir ~/out/align --baseprefix $S5/examples

* Check if the output BAMs and QC metrics are produced

 ls ~/out/align/bams

 ls ~/out/align/QCFiles/

=== Understanding the Output Files ===

* To see the content of BAM file in the format of SAM specification, try

  samtools view -h ~/out/align/bams/NA06984.recal.bam | less

* Check the summary QC metrics 

 cat ~/out/align/QCFiles/NA06984.qplot.stats

* Check whether the sample is contaminated from [[verifyBamID]] output

 cat ~/out/align/QCFiles/NA06984.genoCheck.selfSM

 cat ~/out/align/QCFiles/NA12878.genoCheck.selfSM