Changes

The fastq files are processed using the 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 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 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 alignment pipeline, the base qualities are adjusted to more accurately reflect the likelihood that the base is correct.  

The 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.

The variant calling pipeline processes the deduped and recalibrated BAMs file 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 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 BAMs file 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 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.

After completing the GotCloud Variant Calling Pipeline, [[EPACTS|EPACTS (Efficient and Parallelizable Association Container Toolbox)]] can be used to perform statistical tests to identify genome-wide association from sequence data.

After completing the GotCloud Variant Calling Pipeline, [[EPACTS|EPACTS (Efficient and Parallelizable Association Container Toolbox)]] can be used to perform statistical tests to identify genome-wide association from sequence data.