Changes between Version 41 and Version 42 of SnpCallingPipeline

Timestamp:

Oct 18, 2010 4:43:35 AM (14 years ago)

Author:

Morris Swertz

Comment:

--

SnpCallingPipeline

@@ -140 +140 @@
 ||doc:    ||http://www.broadinstitute.org/gsa/wiki/index.php/Local_realignment_around_indels#Running_the_Indel_Realigner_only_at_known_sites ||
 
-== Workflow 2: Alignment per Lane, per Chr ==
 
-This workflow aligns reads per lane and chromosome, including:
-* re-alignment to prevend false SNP calls caused by indels (using known indels)
-* markduplicates to prevend false coverage caused by PCR errors (per library = lane)
-* base quality recalibration to correct for false low scores caused by true variation
-
-Workflow Inputs:
-* lane.1.fq.gz - raw reads for lane, pair end 1
-* lane.2.fq.gz - raw reads for lane, pair end 2
-* genome.chr.fasta - reference genome split on chromosome
-* genome.chr.realign.intervals - targets for realignment per chromosome
-* genome.chr.dbsnpXYZ.rod - known snp variants, here from dpbsnp
-* genome.chr.indelsXYZ.vcf - known indels from, here from 1KG 
-
-Workflow ouputs:
-* lane.chr.1.sai - alignment index for first pair
-* lane.chr.2.sai - alignment index for second pair
-* lane.chr.sam - alignment map for
-* lane.chr.bam - alignment map in binary format
-* lane.chr.sorted.bam - sorted alignment map
-* lane.chr.sorted.bai - sorted alignment index
-* lane.chr.dedup.bam - marked duplicate PCR elements
-* lane.chr.dedup.metrics - metrics describing deduplication
-* lane.chr.realigned.bam - realigned based on known indels
-* lane.chr.matefixed.bam - fixed the mate pair ends
-* lane.chr.covariate_table.csv - table of countcovariates output for recalibration
-* lane.chr.recal.bam - alignment map with recalibrated quality scores
-
-=== align ===
-Align each end of paired end.
- 
-||tool:   ||bwa-align ||
-||input:  ||chr.fasta, lane.1.fq.gz, lane.2.fq.gz ||
-||output: ||lane.chr.1.sai, lane.chr.2.sai ||
-||docs:   ||http://bio-bwa.sourceforge.net/bwa.shtml ||
-
-=== align-pe ===
-Align the pairs as one
-
-||tool:    ||bwa sampe || 
-||inputs:  ||chr.fasta [[BR]] lane.1.fq.gz [[BR]] lane.2.fq.gz [[BR]] lane.chr.1.sai [[BR]] lane.chr.2.sai ||
-||outputs: ||lane.chr.sam ||
-||docs:    ||http://bio-bwa.sourceforge.net/bwa.shtml ||
-
-=== sam-to-bam ===
-Convert sam to bam
-
-||tool:    ||samtools view || 
-||inputs:  ||lane.chr.sam ||
-||outputs: ||lane.chr.bam ||
-||docs:    ||http://samtools.sourceforge.net/samtools.shtml ||
-
-(Question: can this not index and sort?)
-
-=== sam-sort ===
-Sort bam file on coordinate
-
-||tool:    ||samtools sort || 
-||inputs:  ||lane.chr.bam ||
-||outputs: ||lane.chr.sorted.bam ||
-||docs:    ||http://samtools.sourceforge.net/samtools.shtml ||
-
-=== sam-index ===
-Index bam file for quicker access
-
-||tool:    ||samtools index ||
-||inputs:  ||lane.chr.sorted.bam ||
-||outputs: ||lane.chr.sorted.bai ||
-||docs:    ||http://samtools.sourceforge.net/samtools.shtml ||
-
-=== !MarkDuplicates ===
-Mark duplicate PCR fragments to be filtered in analysis
-
-||tool:    ||MarkDuplicates.jar ||
-||inputs:  ||lane.chr.sorted.bam ||
-||outputs: ||lane.chr.dedup.bam [[BR]] lane.chr.dedup.metrics ||
-||docs:    ||http://picard.sourceforge.net/command-line-overview.shtml#MarkDuplicates ||
-
-=== !IndelRealigner-!KnownsOnly ===
-Improve the alignment using known indel information (will reduce false SNP calls)
-
-||tool:    ||GenomeAnalysisTK.jar -T IndelRealigner ||
-||inputs:  ||lane.chr.dedup.bam [[BR]] genome.chr.realign.intervals [[BR]] genome.chr.dbsnpXYZ.rod [[BR]] genome.chr.indelsXYZ.vcf ||
-||outputs: ||lane.chr.realigned.bam ||
-||docs     ||http://www.broadinstitute.org/gsa/wiki/index.php/Local_realignment_around_indels#Running_the_Indel_Realigner_only_at_known_sites ||
-
-=== !FixMateInformation ===
-Fix the paired end information as consequence of the realignment.
-
-||tool:    ||FixMateInformation.jar ||
-||inputs:  ||lane.chr.realigned.bam
-||outputs: ||lane.chr.matefixed.bam ||
-||docs:    ||http://picard.sourceforge.net/command-line-overview.shtml#FixMateInformation, 
-
-http://www.broadinstitute.org/gsa/wiki/index.php/Local_realignment_around_indels#Fixing_Mate_Pairs ||
-
-=== !CountCovariates ===
-Count covariants, such as machine cycle and bp position, to be used as basis for quality recalibration.
-Optionally: plot the results to pdf using AnalyzeCovariates
-
-||tool:    ||GenomeAnalysisTK.jar -T CountCovariates, AnalyzeCovariates.jar ||
-||inputs:  ||lane.chr.matefixed.bam [[BR]] genome.chr.dbsnpXYZ.rod ||
-||outputs: ||lane.chr.covariate_table.csv ||
-||docs:    ||http://www.broadinstitute.org/gsa/wiki/index.php/Base_quality_score_recalibration#CountCovariates [[BR]]
-
-http://www.broadinstitute.org/gsa/wiki/index.php/Base_quality_score_recalibration#AnalyzeCovariates.jar ||
-
-=== !TableRecalibration ===
-Recalibrate quality scores based on the covariate table
-||tool:    ||GenomeAnalysisTK.jar -T TableRecalibration ||
-||inputs:  ||lane.chr.matefixed.bam [[BR]]lanec.chr.recal_table.csv [[BR]]chr.fasta || 
-||outputs: ||lane.chr.recal.bam
-||docs:    ||http://www.broadinstitute.org/gsa/wiki/index.php/Base_quality_score_recalibration#TableRecalibration ||
-
-=== Repeat: sam-sort, sam-index, countcovariates ===
-See steps above for commands and docs.
-
-||inputs:  ||lane.chr.recal.bam ||
-||outputs: ||lane.chr.recal.sorted.bam, lane.chr.recal.sorted.bam.bai, lane.chr.recal.covariate_table.csv ||
-
-Discussion:
-> wy do we need to sort and index after recalibration? does it mess up the order of things?
-