Whole Exome Sequencing Analysis Pipeline

= Whole Exome Sequencing Analysis Pipeline =



The pipeline contains the following steps:


 * 1) Global config  : Set up global configuration of the pipeline.

mapping

 * 1) Mapping : Align short sequences to the human reference genome sequence database.
 * 2) Fixmate : Fixing the mate pairs information to ensure that all mate-pair information is in sync between each read and it's mate pair.

filtering

 * 1) Filter : Filtering for mapping, pairing, and proper paired
 * 2) Remove duplicate : Examines aligned records in the BAM file to locate duplicate reads and remove them.
 * 3) Filter low mapping quality : Filter low mapping quality reads

realign/recalibration

 * 1) Create intervals : Collect regions around potential indels and clusters of mismatches. Determine small suspicious intervals which are likely in need of realignment.
 * 2) Realignment : Run the realigner over the intervals to create a cleaned version of the BAM file.
 * 3) Analysis of covariates : Determine the covariates affecting base quality scores in the BAM file.
 * 4) Recalibration : Walking through the BAM file and rewrite the quality scores.
 * 5) Recalculate analysis of covariates : Determine the covariates affecting base quality scores in the realigned recalibrated BAM file for the comparison.
 * 6) Depth of coverage : Determine coverage summarized by mean, median, quartiles, and/or percentage of bases covered.
 * 7) DoC for genes : Determine coverage on genes
 * 8) HsMetrics : Calculates a set of Hybrid Selection specific metrics from an aligned BAM file..
 * 9) Cleanup : Remove all intermediate alignment and BAM files. Keep only first aligned and last realigned-recalibrated BAM files.

variant calling

 * 1) Calling variants
 * 2) *Generate snps raw vcf file
 * 3) *Generate indels raw vcf file
 * 4) *Variant filtration generate indels and indels.PASS files
 * 5) *Variant filtration generate snps and snps.PASS files
 * 6) *evaluating snps
 * 7) Group Calling and Variant Recalibration
 * 8) *UnifiedGenotyper Group Calling
 * 9) *Variant Recalibration
 * 10) *Apply Recalibration
 * 11) *Variant_Evaluation
 * 12) Generate genotype
 * 13) Annotation snpEff
 * 14) Annotation Annovar

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