Tutorial: GotCloud UW CMG - Revision history

Hmkang: /* STEP 5 : All-in-one running of all scripts (for later use) */

2013-08-06T20:15:27Z

STEP 5 : All-in-one running of all scripts (for later use)

← Older revision		Revision as of 16:15, 6 August 2013
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	== STEP 5 : All-in-one running of all scripts (for later use) ==		== STEP 5 : All-in-one running of all scripts (for later use) ==

	% tar xzvf /home/presenter02/day2/session1/uwcmg_2013_08.tar.~~gz�~~		% tar xzvf /home/presenter02/day2/session1/uwcmg_2013_08.tar.gz

	% cd /home/presenter02/day2/session1/~~uwcmg_2013_08�~~		% cd /home/presenter02/day2/session1/uwcmg_2013_08

	% sh go.sh �		% sh go.sh

Hmkang: /* STEP 4 : EPACTS association analysis */

2013-08-06T20:12:23Z

STEP 4 : EPACTS association analysis

Show changes

Hmkang: /* STEP 4 : EPACTS association analysis */

2013-08-06T20:04:38Z

STEP 4 : EPACTS association analysis

@@ Line 437: / Line 437: @@
 Run single variant logistic score test.
   % ${GC}/epacts/bin/epacts single  --ped ${GC}/examples/index/chr7.CFTR.ped   --vcf ${GC}/out/snps/beagle/chr7/chr7.filtered.PASS.beagled.vcf.gz  --pheno PHENO --out assoc/single.b.score --test b.score --anno   --ref ${GC}/examples/chr7Ref/hs37d5.chr7.fa   --region 7:117000000-117500000 --run 1
   % time ${GC}/epacts/bin/epacts anno --in ${GC}/out/snps/beagle/chr7/chr7.filtered.PASS.beagled.vcf.gz --out snps/chr7.filtered.PASS.beagled.anno.vcf.gz --ref ${GC}examples/chr7Ref/hs37d5.chr7.fa

Hmkang: /* Step 1 : GotCloud Alignment Pipeline */

2013-08-06T19:49:35Z

Step 1 : GotCloud Alignment Pipeline

← Older revision		Revision as of 15:49, 6 August 2013
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	NA06984.recal.bam NA06984.recal.bam.bai.done NA06984.recal.bam.metrics NA12878.recal.bam NA12878.recal.bam.bai.done NA12878.recal.bam.metrics		NA06984.recal.bam NA06984.recal.bam.bai.done NA06984.recal.bam.metrics NA12878.recal.bam NA12878.recal.bam.bai.done NA12878.recal.bam.metrics
	NA06984.recal.bam.bai NA06984.recal.bam.done NA06984.recal.bam.qemp NA12878.recal.bam.bai NA12878.recal.bam.done NA12878.recal.bam.qemp		NA06984.recal.bam.bai NA06984.recal.bam.done NA06984.recal.bam.qemp NA12878.recal.bam.bai NA12878.recal.bam.done NA12878.recal.bam.qemp

			You can view the aligned sequence reads by running
			% samtools view align/bams/NA06984.recal.bam \| less

	Examine the QC metrics by		Examine the QC metrics by

Hmkang: /* Step 1 : GotCloud Alignment Pipeline */

2013-08-06T17:39:27Z

Step 1 : GotCloud Alignment Pipeline

← Older revision		Revision as of 13:39, 6 August 2013
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	SRR035022_2.fastq.gz SRR035023_2.fastq.gz SRR035024_2.fastq.gz SRR035025_2.fastq.gz SRR035026_2.fastq.gz SRR035027_2.fastq.gz SRR035669_2.fastq.gz SRR622461_2.fastq.gz		SRR035022_2.fastq.gz SRR035023_2.fastq.gz SRR035024_2.fastq.gz SRR035025_2.fastq.gz SRR035026_2.fastq.gz SRR035027_2.fastq.gz SRR035669_2.fastq.gz SRR622461_2.fastq.gz
	SRR035022.fastq.gz SRR035023.fastq.gz SRR035024.fastq.gz SRR035025.fastq.gz SRR035026.fastq.gz SRR035027.fastq.gz SRR035669.fastq.gz SRR622461.fastq.gz		SRR035022.fastq.gz SRR035023.fastq.gz SRR035024.fastq.gz SRR035025.fastq.gz SRR035026.fastq.gz SRR035027.fastq.gz SRR035669.fastq.gz SRR622461.fastq.gz

			To see examples of FASTQ file.
			% zless ${GC}/examples/fastq/SRR035022_1.fastq.gz

	This set of FASTQ are extracted from two samples from the 1000 Genomes project, focusing around 500kb region are CFTR.		This set of FASTQ are extracted from two samples from the 1000 Genomes project, focusing around 500kb region are CFTR.

Hmkang: /* STEP 4 : EPACTS association analysis */

2013-08-06T16:59:07Z

STEP 4 : EPACTS association analysis

@@ Line 410: / Line 410: @@
 == STEP 4 : EPACTS association analysis  ==
   % mkdir assoc
-  % time ${GC}/epacts/bin/epacts single  --ped ${GC}/examples/index/chr7.CFTR.ped   --vcf ${GC}/out/snps/beagle/chr7/chr7.filtered.PASS.beagled.vcf.gz  --pheno PHENO --out assoc/single.b.score --test b.score --anno   --ref ${GC}/examples/chr7Ref/hs37d5.chr7.fa   --region 7:117000000-117500000 --run 1
+Run single variant logistic score test.
   % time ${GC}/epacts/bin/epacts anno --in ${GC}/out/snps/beagle/chr7/chr7.filtered.PASS.beagled.vcf.gz --out snps/chr7.filtered.PASS.beagled.anno.vcf.gz --ref ${GC}examples/chr7Ref/hs37d5.chr7.fa

Hmkang: /* STEP 3 : Run GotCloud SNP Calling Pipeline */

2013-08-06T16:46:55Z

STEP 3 : Run GotCloud SNP Calling Pipeline

@@ Line 182: / Line 182: @@
   ...
   % cat ${GC}/examples/index/chr7.CFTR.low_coverage.index
   NA06984	EUR	bams/NA06984.mapped.ILLUMINA.bwa.CEU.low_coverage.20120522.CFTR.bam
@@ Line 195: / Line 197: @@
   ...
   % cat ${GC}/examples/index/chr7.CFTR.low_coverage.conf
@@ Line 208: / Line 211: @@
   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
   % ${GC}/gotcloud/gotcloud snpcall --conf ${GC}/examples/index/chr7.CFTR.low_coverage.conf --outDir snps --baseprefix ${GC}/examples --region 7:117000000-117500000 --numjobs 2
   CHRS = 7
   BAM_INDEX = index/chr7.CFTR.low_coverage.index
@@ Line 345: / Line 349: @@
    Commands finished in 306 secs with no errors reported
   --------------------------------------------------------------------
   % cat ${GC}/out/snps/vcfs/chr7/chr7.filtered.sites.vcf.summary
@@ Line 368: / Line 374: @@
   ------------------------------------------------------------------------------------------------------------
- % ${GC}/gotcloud/gotcloud beagle --conf ${GC}/examples/index/chr7.CFTR.low_coverage.conf --outDir snps --baseprefix ${GC}/examples --region 7:117000000-117500000 --numjobs 2
+If you're interested in looking at individual reads from the variant, samtools tview provides a good alternative to IGV. In order to see CFTR R75Q variant in one of the variant carriers, you can run
   % samtools tview ${GC}/examples/bams/NA12843.mapped.ILLUMINA.bwa.CEU.low_coverage.20130415.CFTR.bam ${GC}/examples/chr7Ref/hs37d5.chr7.fa
 == STEP 4 : EPACTS association analysis  ==

Hmkang: /* STEP 3 : Run GotCloud SNP Calling Pipeline */

2013-08-06T16:39:38Z

STEP 3 : Run GotCloud SNP Calling Pipeline

← Older revision		Revision as of 12:39, 6 August 2013
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	% cat ${GC}/out/snps/vcfs/chr7/chr7.filtered.sites.vcf.summary		% cat ${GC}/out/snps/vcfs/chr7/chr7.filtered.sites.vcf.summary
	~~cat ${GC}/out/snps/vcfs/chr7/chr7.filtered.sites.vcf.summary~~
	--------------------------------------------------------------------------------------------------------------		--------------------------------------------------------------------------------------------------------------
	FILTER #SNPs #dbSNP %dbSNP %CpG %CpG %Known %Novel %nCpG-K %nCpG-N %HM3 %HM3		FILTER #SNPs #dbSNP %dbSNP %CpG %CpG %Known %Novel %nCpG-K %nCpG-N %HM3 %HM3
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	% ~~time~~ ${GC}/gotcloud/gotcloud beagle --conf ${GC}/examples/index/chr7.CFTR.low_coverage.conf --outDir snps --baseprefix ${GC}/examples --region 7:117000000-117500000 --numjobs 2		% ${GC}/gotcloud/gotcloud beagle --conf ${GC}/examples/index/chr7.CFTR.low_coverage.conf --outDir snps --baseprefix ${GC}/examples --region 7:117000000-117500000 --numjobs 2

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

Hmkang: /* STEP 3 : Run GotCloud SNP Calling Pipeline */

2013-08-06T16:37:15Z

STEP 3 : Run GotCloud SNP Calling Pipeline

Show changes

Hmkang: /* STEP 3 : Run GotCloud SNP Calling Pipeline */

2013-08-06T16:21:47Z

STEP 3 : Run GotCloud SNP Calling Pipeline

@@ Line 167: / Line 167: @@
   % ls ${GC}/examples/bams
   % cat ${GC}/examples/index/chr7.CFTR.low_coverage.index
   % cat ${GC}/examples/index/chr7.CFTR.low_coverage.conf
-  % time ${GC}/gotcloud/gotcloud snpcall --conf ${GC}/examples/index/chr7.CFTR.low_coverage.conf --outDir snps --baseprefix ${GC}/examples --region 7:117000000-117500000 --numjobs 2
+  % ${GC}/gotcloud/gotcloud snpcall --conf ${GC}/examples/index/chr7.CFTR.low_coverage.conf --outDir snps --baseprefix ${GC}/examples --region 7:117000000-117500000 --numjobs 2
   % cat ${GC}/out/snps/vcfs/chr7/chr7.filtered.sites.vcf.summary
   % time ${GC}/gotcloud/gotcloud beagle --conf ${GC}/examples/index/chr7.CFTR.low_coverage.conf --outDir snps --baseprefix ${GC}/examples --region 7:117000000-117500000 --numjobs 2