1,120
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchTutorial: EMMAX GotCloud STOM: Lecture 5 (view source)
Revision as of 03:30, 6 January 2014
, 03:30, 6 January 2014Created page with "STOM 2014 Workshop - Practical Sessions 5 == Lecture 5 == The slides describing the notes below are available here (PDF) === Basic Setup ==..."
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
== 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
