Tutorial: EMMAX GotCloud STOM: Lecture 6 - Revision history

Hmkang: /* Preparing Input Files */

2014-01-06T13:58:20Z

Preparing Input Files

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

	CHRS = 7		CHRS = 7

Hmkang: /* Running LD-aware genotype refinement */

2014-01-06T13:58:04Z

Running LD-aware genotype refinement

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	(WARNING: This step will take a long time, up to 2 minutes)		(WARNING: This step will take a long time, up to 2 minutes)

	time $S5/gotcloud/gotcloud beagle --conf � $S5/examples/index/chr7.CFTR.low_coverage.conf � --outDir ~/out/snps --baseprefix $S5/examples � --region 7:117000000-117500000 --numjobs 2		time $S5/gotcloud/gotcloud beagle --conf $S5/examples/index/chr7.CFTR.low_coverage.conf --outDir ~/out/snps --baseprefix $S5/examples --region 7:117000000-117500000 --numjobs 2

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

Hmkang: /* Run GotCloud SNP calling Pipeline */

2014-01-06T13:57:32Z

Run GotCloud SNP calling Pipeline

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	(WARNING: This step will take a long time, up to 5 minutes, because it processes nearly 100 BAMs, 4 jobs simultaneously at a time)		(WARNING: This step will take a long time, up to 5 minutes, because it processes nearly 100 BAMs, 4 jobs simultaneously at a time)

	time $S5/gotcloud/gotcloud snpcall --conf � $S5/examples/index/chr7.CFTR.low_coverage.conf � --outDir ~/out/snps --baseprefix $S5/examples � --region 7:117000000-117500000 --numjobs 4		time $S5/gotcloud/gotcloud snpcall --conf $S5/examples/index/chr7.CFTR.low_coverage.conf --outDir ~/out/snps --baseprefix $S5/examples --region 7:117000000-117500000 --numjobs 4

	* Check the summary statistics of SNP call to evaluate its quality		* Check the summary statistics of SNP call to evaluate its quality

Hmkang: Created page with "STOM 2014 Workshop - Practical Sessions 6 == Lecture 6 == The slides describing the notes below are available here (PDF) === Basic Setup ==..."

2014-01-06T08:10:15Z

Created page with "STOM 2014 Workshop - Practical Sessions 6 == Lecture 6 == The slides describing the notes below are available here (PDF) === Basic Setup ==..."

New page

STOM 2014 Workshop - Practical Sessions 6

== Lecture 6 ==

The slides describing the notes below are available [[Media:Stom practice 06.pdf | here (PDF)]]

=== Basic Setup ===

If you still have the logged in console from lecture 5 practical session, you may skip this part

* 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

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

=== Preparing Input Files ===

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

less $S5/examples/index/chr7.CFTR.low_coverage.index

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

CHRS = 7
BAM_INDEX = index/chr7.CFTR.low_coverage.index
############
# References
REF_ROOT = chr7Ref
#
REF = $(REF_ROOT)/hs37d5.chr7.fa
INDEL_PREFIX = $(REF_ROOT)/1kg.pilot_release.merged.indels.sites.hg19
DBSNP_VCF = $(REF_ROOT)/dbsnp_135.b37.chr7.CFTR.vcf.gz
HM3_VCF = $(REF_ROOT)/hapmap_3.3.b37.sites.chr7.CFTR.vcf.gz
OMNI_VCF = $(REF_ROOT)/1000G_omni2.5.b37.sites.PASS.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 SNP calling Pipeline ===

* Using the prepared input files, call SNPs using the gotcloud SNP calling pipeline

(WARNING: This step will take a long time, up to 5 minutes, because it processes nearly 100 BAMs, 4 jobs simultaneously at a time)

time $S5/gotcloud/gotcloud snpcall --conf � $S5/examples/index/chr7.CFTR.low_coverage.conf � --outDir ~/out/snps --baseprefix $S5/examples � --region 7:117000000-117500000 --numjobs 4

* Check the summary statistics of SNP call to evaluate its quality

cat ~/out/snps/vcfs/chr7/chr7.filtered.sites.vcf.summary

=== Running LD-aware genotype refinement ===

(WARNING: This step will take a long time, up to 2 minutes)

time $S5/gotcloud/gotcloud beagle --conf � $S5/examples/index/chr7.CFTR.low_coverage.conf � --outDir ~/out/snps --baseprefix $S5/examples � --region 7:117000000-117500000 --numjobs 2

=== Understanding the Output Files ===

* To see the content of VCF file, try

zless ~/out/snps/beagle/chr7/chr7.filtered.PASS.beagled.vcf.gz

* If you want to look at a variant at a particular genomic position or in a particular genomic region, use the tabix utility to facilitate random access without reading the whole VCF file.

$S5/epacts/bin/tabix ~/out/snps/beagle/chr7/chr7.filtered.PASS.beagled.vcf.gz 7:117149147-117149147

The example above displays known CFTR risk variant, R75Q

=== Using samtools to visualize the sequence reads and verify the variant calls ===

samtools tview $S5/examples/bams/NA12843.mapped.ILLUMINA.bwa.CEU.low_coverage.20130415.CFTR.bam $S5/examples/chr7Ref/hs37d5.chr7.fa

After running this.. try to
# Type 'g'
# Type '7:117149147'
# Type 'n' to change the display (color by nucleotide)
# Move with left arrow to see the variant site clearly