Changes

[[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]]

== GotCloud Setup ==

== GotCloud Setup ==