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[[File:Gotcloud.puzzles.v2.png|500px]]
[[File:Gotcloud.puzzles.v2.png|500px]]
=== Getting Help with GotCloud ===
=== Getting Help with GotCloud ===
The fastq files are processed using the [[GotCloud: Alignment Pipeline|alignment pipeline]] which finds the most likely genomic location for each read and stores that information in a [[BAM|BAM (Binary Sequence Alignment/Map format) file]]. In addition to the sequence and base quality information contained in FASTQ files, a BAM file also contains the genomic location and some additional information about the mapping. As part of the [[GotCloud: Alignment Pipeline|alignment pipeline]], the base qualities are adjusted to more accurately reflect the likelihood that the base is correct.
The fastq files are processed using the [[GotCloud: Alignment Pipeline|alignment pipeline]] which finds the most likely genomic location for each read and stores that information in a [[BAM|BAM (Binary Sequence Alignment/Map format) file]]. In addition to the sequence and base quality information contained in FASTQ files, a BAM file also contains the genomic location and some additional information about the mapping. As part of the [[GotCloud: Alignment Pipeline|alignment pipeline]], the base qualities are adjusted to more accurately reflect the likelihood that the base is correct.
The [[GotCloud: Alignment Pipeline|alignment pipeline]] can be skipped if you already have Deduped and Recalibrated BAM files.
The [[GotCloud: Alignment Pipeline|alignment pipeline]] can be skipped if you already have Deduped and Recalibrated BAM files. If you have BAMs, but they needed to be deduped and recalibrated, you can use our [[GotCloud:_Alignment_Sub-Pipelines#recabQC_2|recabQC pipeline]].
The [[GotCloud: Variant Calling Pipeline|variant calling pipeline]] processes the deduped and recalibrated BAM files produced by the alignment pipeline or that you provide it, generating an initial list of polymorphic sites and genotypes stored in a [http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41 VCF (Variant Call Format) file]. The [[GotCloud: Variant Calling Pipeline|variant calling pipeline]] then filters the variants using both hard filters and a [[SVM Filtering|Support Vector Machine (SVM)]]. It then uses haplotype information to refine these genotypes in an updated VCF file.
The [[GotCloud: Variant Calling Pipeline|variant calling pipeline]] processes the deduped and recalibrated BAM files produced by the alignment pipeline or that you provide it, generating an initial list of polymorphic sites and genotypes stored in a [http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41 VCF (Variant Call Format) file]. The [[GotCloud: Variant Calling Pipeline|variant calling pipeline]] then filters the variants using both hard filters and a [[SVM Filtering|Support Vector Machine (SVM)]]. It then uses haplotype information to refine these genotypes in an updated VCF file.
[[File:GotCloudDiagram.jpg|500px]]
[[File:GotCloudDiagram.jpg|500px]]
== Publication ==
If you use GotCloud, please cite our publication:
[http://genome.cshlp.org/content/early/2015/04/14/gr.176552.114.abstract Jun, Goo, et al. "An efficient and scalable analysis framework for variant extraction and refinement from population scale DNA sequence data." Genome research (2015): gr-176552.]
== GotCloud Setup ==
== GotCloud Setup ==
** You can run on an EC2 cluster instance created by StarCluster.
** You can run on an EC2 cluster instance created by StarCluster.
GotCloud has been developed and tested on Linux Ubuntu 12.10 and 12.04.2 LTS. While it should work on other Linux systems, they have not yet been tested.
GotCloud has been developed and tested on Linux Ubuntu 12.10 and 12.04.2 LTS and Red Hat 6.6. While it should work on other Linux systems, they have not yet been tested.
=== GotCloud on Amazon ===
=== GotCloud on Amazon ===
** [[GotCloud: Alignment Sub-Pipelines|Alignment Sub-Pipelines]] - for if you do not want to run the entire Alignment Pipeline
** [[GotCloud: Alignment Sub-Pipelines|Alignment Sub-Pipelines]] - for if you do not want to run the entire Alignment Pipeline
* [[GotCloud: Variant Calling Pipeline|Variant Calling Pipeline]]
* [[GotCloud: Variant Calling Pipeline|Variant Calling Pipeline]]
* [[GotCloud: Indel Calling Pipeline|Indel Calling Pipeline]]
* Indel Calling Pipeline
* [[GotCloud: GenomeSTRiP Pipeline|GenomeSTRiP Pipeline]] (Structural Variation) - ''Coming Soon''
* [[GotCloud: GenomeSTRiP Pipeline|GenomeSTRiP Pipeline]] (Structural Variation)
* [[GotCloud: MEI Calling Pipeline|MEI Calling Pipeline]] - ''Coming Soon''
* MEI Calling Pipeline - ''Ask if you're interested''
You can also create your own pipelines. Instructions are here:
You can also create your own pipelines. Instructions are here:
