Tutorial: EMMAX GotCloud STOM: Lecture 5

STOM 2014 Workshop - Practical Sessions 5

Lecture 5

The slides describing the notes below are available 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