Tutorial: EMMAX GotCloud STOM: Lecture 5 - Revision history

Hmkang: /* Preparing Input Files */

2014-01-06T14:07:41Z

Preparing Input Files

← Older revision		Revision as of 10:07, 6 January 2014
Line 33:		Line 33:
	* Configuration File - See the example configuration file below.		* Configuration File - See the example configuration file below.
	cat $S5/examples/index/chr7.CFTR.align.conf		cat $S5/examples/index/chr7.CFTR.align.conf

	INDEX_FILE = index/chr7.CFTR.fastq.index		INDEX_FILE = index/chr7.CFTR.fastq.index
	###################		###################

Hmkang: /* Preparing Input Files */

2014-01-06T14:07:21Z

Preparing Input Files

← Older revision		Revision as of 10:07, 6 January 2014
Line 32:		Line 32:

	* Configuration File - See the example configuration file below.		* Configuration File - See the example configuration file below.
	% cat $S5/examples/index/chr7.CFTR.align.conf		cat $S5/examples/index/chr7.CFTR.align.conf

	INDEX_FILE = index/chr7.CFTR.fastq.index		INDEX_FILE = index/chr7.CFTR.fastq.index

Hmkang at 08:02, 6 January 2014

2014-01-06T08:02:08Z

← Older revision		Revision as of 04:02, 6 January 2014
Line 29:		Line 29:
	* Index file - See the example index file already prepared for this project		* Index file - See the example index file already prepared for this project

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

	* Configuration File - See the example configuration file below.		* Configuration File - See the example configuration file below.

Hmkang: /* Run GotCloud Alignment Pipeline */

2014-01-06T07:31:25Z

Run GotCloud Alignment Pipeline

← Older revision		Revision as of 03:31, 6 January 2014
Line 49:		Line 49:
	* Using the prepared input files, align the FASTQ files using the 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		$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		* Check if the output BAMs and QC metrics are produced

	ls ~/out/align/~~bams�~~		ls ~/out/align/bams

	ls ~/out/align/QCFiles/�		ls ~/out/align/QCFiles/

	=== Understanding the Output Files ===		=== Understanding the Output Files ===

Hmkang: /* Preparing Input Files */

2014-01-06T07:31:05Z

Preparing Input Files

← Older revision		Revision as of 03:31, 6 January 2014
Line 32:		Line 32:

	* Configuration File - See the example configuration file below.		* Configuration File - See the example configuration file below.
	% cat $S5/examples/index/chr7.CFTR.align.~~conf�~~		% cat $S5/examples/index/chr7.CFTR.align.conf

	~~�INDEX_FILE~~ = index/chr7.CFTR.fastq.index		INDEX_FILE = index/chr7.CFTR.fastq.index
	###################		###################
	# References		# References
Line 44:		Line 44:

	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		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 ===		=== Run GotCloud Alignment Pipeline ===

Hmkang: Created page with "STOM 2014 Workshop - Practical Sessions 5 == Lecture 5 == The slides describing the notes below are available here (PDF) === Basic Setup ==..."

2014-01-06T07:30:43Z

Created page with "STOM 2014 Workshop - Practical Sessions 5 == Lecture 5 == The slides describing the notes below are available here (PDF) === Basic Setup ==..."

New page

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