2. What is genomesontheCloud ?
gotCloud is a sequence analysis pipeline
Integrative Alignment, QC, Variant Calling, Phasing
Seamless Requires only simple configuration files
Robust ..against unexpected failures & stops
Scalable ..to many thousands of genomes
gotCloud also provides…
A set of many useful software tools
Software library (C++) for sequence analysis
Briefly Talk about software tools and library included in GotCloud

3. How can I use
gotCloud?
Briefly Talk about software tools and library included in GotCloud

4. GotCloud Alignment Pipeline
& QC
Single
Sample
Many
Samples
GotCloud Alignment Pipeline
qplot &
verifyBamID
bwa / mosaik
dedup & recab
Processed BAM
(one per sample)
FASTQ
Raw BAM
(one per sample) QC
End-to-end analysis
Fully automated and parallelized (with quality controls)
Requires only a simple fastq list file
SAMPLE_ID
FASTQ1
FASTQ2
Sample1
Sm1_Run1_1.fastq.gz
Sm1_Run2_1.fastq.gz
Sample2
Sm2.fastq.gz .
Sample3
Sm3_1.fastq.gz
Sm3_2.fastq.gz

5. Running GotCloud Alignment Pipeline
& QC
Single
Sample
Many
Samples
Example command
./gotcloud align --list fastq.txt --out outputDir --numjobs 3 --threads 2
./gotcloud run GotCloud
align alignment pipeline
--list fastq.txt list of FASTQs
--out outputDir where to write output
--numjobs 3 run 3 samples concurrently
--threads CPU threads per sample
CRAM support is in beta testing

6. What to Expect from GotCloud Alignment Pipeline
& QC
Single
Sample
Many
Samples
Aligned and post-processed BAM files
Summary statistics and graphs from qplot
Contamination checking from verifyBamID
With and/or without external genotype data
Base
Quality
GC-bias
Insert Size

7. GotCloud Variant Calling Pipelines
Filtering
Haplotyping
Deep
Genomes
Shallow
Genomes
Targeted
Exomes
Overview of SNP Calling Pipeline
Processed BAM
(one per sample)
Genotype Likelihood (one per sample)
Single
Sample
Many
Samples
samtools
End-to-end analysis
Very efficient
Small memory (<1G)
Scalable to >1,000s
High parallelization
Fault-tolerant
Requires only list of BAMs
glfMultiples
infoCollector
Filtered
VCF
Unfiltered VCF
SVM
beagle
/ thunder
Phased
VCF
Association Results
EPACTS
(External)

8. GotCloud Variant Calling Pipelines
SNPs
Indels
Structural
Variants
Deep
Genomes
Shallow
Genomes
Targeted
Exomes
Example commands
./gotcloud snpcall list bams.txt --out outputDir --numjobs 10
./gotcloud indel list bams.txt --out outputDir --numjobs 10
./gotcloud genomestrip --list bams.txt --out outputDir --numjobs 10
./gotcloud ldefine list bams.txt --out outputDir --numjobs 10
./gotcloud mei list bams.txt --out outputDir --numjobs 10*
snpcall/indel/genomestrip/mei variant caller to run
ldrefine run beagle/thunderVCF genotype refinement
--list bams.txt list of bams per sample
--out outputDir where to write output
--numjobs 10 run 10 jobs concurrently
* Coming soon..

9. GotCloud for Large-scale Sequencing
Variant
Calling
Variant
Filtering
Many
Samples
Study
Genome
Exome N
Populations
# SNPs
1000 Genomes
~6x
~40x
2,535
Many
69.1M
Type 2 Diabetes
~5x
~80x
2,850
Europeans
26.7M
Exome Sequencing Project .
6,916
EUR+AFR
1.92M
Sardinian Sequencing
~4x
3,520
Sardinians
23.1M
Bipolar Sequencing
~12x
2,825
43.7M
Nephrotic Syndrome
464
25.6M
Age-related Macular Degeneration
3,000
36.2M
HUNT
1,200
Norwegians
23.0M

10. clinically important variants using gotCloud?
Can I detect
clinically important variants using gotCloud?
Briefly Talk about software tools and library included in GotCloud

11. Variant Call Examples using GotCloud
SNPs
Indels
Structural
Variants
Deep
Genomes
Shallow
Genomes
Targeted
Exomes
Examples from APOL1 gene
Nephrotic syndrome associated genes
Available at
SNPs : Nephrotic syndrome risk allele – APOL G1 allele
A G PASS AN=124;AC=2;AF= …
Indels : Nephrotic syndome risk allele – APOL G2 allele
AATAATT A PASS AN=114;AC=2;AF= …
Structural Variants nearby APOL1 loci
C <DEL> . PASS AN=124;AC=2;END=

12. Variant Call Examples using GotCloud
SNPs
Indels
Structural
Variants
Deep
Genomes
Shallow
Genomes
Targeted
Exomes
Examples from APOL1 gene
Nephrotic syndrome associated genes
Available at
SNPs : Nephrotic syndrome risk allele – APOL G1 allele
A G PASS AN=124;AC=2;AF= …
Indels : Nephrotic syndome risk allele – APOL G2 allele
AATAATT A PASS AN=114;AC=2;AF= …
Structural Variants nearby APOL1 loci
C <DEL> . PASS AN=124;AC=2;END=

13. How can I use gotCloud on the Cloud?
Briefly Talk about software tools and library included in GotCloud

14. GotCloud on the Cloud
Alignment
& QC
Variant
Calling
Variant
Filtering
Haplotyping
Deep
Genomes
Shallow
Genomes
Targeted
Exomes
GotCloud supports for many high-computing cluster systems
MOSIX
SLURM
Sun Grid Engine (SGE)
Portable Batch System (PBS)
GotCloud also supports the Amazon Cloud
In 1000G low-pass genomes examples…
Average cost is $20 per genome
GotCloud Amazon Machine Images (AMI) available

15. GotCloud on Amazon Cloud
Alignment
& QC
Variant
Calling
Variant
Filtering
Haplotyping
Deep
Genomes
Shallow
Genomes
Targeted
Exomes
Getting started…
GotCloud AMI is publicly available
The AMI contains example input files
You can run today’s demo on your own
Adding computing power for your own analysis…
GotCloud AMI supports StarCluster (SGE-compatible)
You can add as many nodes as you need.
You will need to upload your own files to Amazon
Have your data mounted or use wget/curl/lftp

16. or https://github.com/statgen/gotcloud
Thanks! or
Gonçalo Abecasis
Adrian Tan
Mary Kate Wing
Terry Gliedt
Hyun Min Kang
Tom Blackwell
Goo Jun
Alan Kwong

17. GotCloud on Amazon Cloud : Launch Amazon Instance
Assuming that you set up your account, security key, and also that you selected GotCloud AMI and machine size (instance type)..
Selected
Instance
Type
Click Launch When Ready

18. GotCloud on Amazon Cloud : Connecting to Your Instance
Click “Connect”
to Launch the terminal
when Ready
After Launching,
Check if the State is “Running”

19. GotCloud on Amazon Cloud : Connecting to Your Instance
Username (e.g. ubuntu)
Path to your key (previously selected)

20. GotCloud on Amazon Cloud : Running GotCloud
List of BAMs per Sample
Check if the demo input files
are available

21. GotCloud on Amazon Cloud : Running GotCloud
Type a GotCloud command line

22. GotCloud on Amazon Cloud : Checking Output Files
Examine the output directory

23. GotCloud on Amazon Cloud : Checking Output Files
Examine the variant of interest

24. GotCloud on Amazon Cloud : Don’t Forget to Terminate