Difference between revisions of "Tutorial: EMMAX GotCloud STOM: Lecture 5"
From Genome Analysis Wiki
Jump to navigationJump to search (Created page with "STOM 2014 Workshop - Practical Sessions 5 == Lecture 5 == The slides describing the notes below are available here (PDF) === Basic Setup ==...") |
|||
| (4 intermediate revisions by the same user not shown) | |||
| 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. | ||
| − | + | cat $S5/examples/index/chr7.CFTR.align.conf | |
| − | + | ||
| − | + | 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 === | ||
| Line 50: | 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 | + | $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/ | + | ls ~/out/align/bams |
| − | ls ~/out/align/QCFiles/ | + | ls ~/out/align/QCFiles/ |
=== Understanding the Output Files === | === Understanding the Output Files === | ||
Latest revision as of 10:07, 6 January 2014
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
