Changes between Version 40 and Version 41 of SnpCallingPipeline

Timestamp:

Oct 18, 2010 4:41:51 AM (15 years ago)

Author:

Morris Swertz

Comment:

--

SnpCallingPipeline

@@ -8 +8 @@
 
 To perform the analysis as fast and good as possible the pipeline has been divided into several small processes. These processes are all numbered and can be found below, including commands, input and output files starting with pre-alignment and ending with variation calling & filtering.
+
+* SnpCallingPipeline/ReferencePreparation
+* SnpCallingPipeline/AlignmentAndCleaning
+* SnpCallingPipeline/VariantCalling
+
 == Simplified Overview ==
 
@@ -259 +264 @@
 > wy do we need to sort and index after recalibration? does it mess up the order of things?
 
-== Workflow 3: sample level variant calling ==
-This workflow will call variants for the samples including:
-* sample level recalibration
-* sample level realignment
-N.B. no sample level MarkDuplicates is needed as lanes == libraries.
-
-Workflow inputs:
-* lane.chr.recal.sorted.bam - for all sample lanes: dedupped, recalibrated, realigned, sorted and indexed bams (3)
-* sample.chip.vcf - genotypes called from genotype chip
-Reference:
-* 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 outputs:
-* sample.chr.bam - merged bam files per sample
-* sample.chr.realign.interval - realignment target intervals
-* sample.chr.realigned.bam - realigned 
-* sample.chr.matesfixed.bam - fixed pairs in realignment
-* sample.chr.indels.vcf - raw indels called
-* sample.chr.indels.bed - raw indels annotations
-* sample.chr.indels.txt - output from the indel calling
-* sample.chr.indels.filtered.bed - indels filtered
-* sample.chr.snps.vcf - raw snps called
-* sample.chr.snps.filtered.vcf - snps filtered
-
-=== merge-lanes ===
-Merge lanes into one sample bam
-
-||tool:    ||sam merge ||
-||inputs:  ||lane.chr.recal.sorted.bam ||
-||outputs: ||sample.chr.bam ||
-||docs:    ||http://samtools.sourceforge.net/samtools.shtml ||
-
-=== !RealignerTargetCreator ===
-Create realignment targets based on the data (so not only knowns)
-
-||tool:    ||GenomeAnalysisTK.jar -T RealignerTargetCreator ||
-||inputs:  ||sample.chr.bam [[BR]]genome.chr.fa [[BR]]dbsnpXYz.chr.rod [[BR]]indelsXYZ.vcf
-||outputs: ||sample.chr.realign.intervals ||
-||doc:     ||http://www.broadinstitute.org/gsa/wiki/index.php/Local_realignment_around_indels#Creating_Intervals ||
-
-=== !IndelRealigner ===
-Realign based on realignment targets in previous step
-
-||tool:    ||GenomeAnalysisTK.jar -T IndelRealigner ||
-||inputs:  ||sample.chr.bam [[BR]]genome.chr.realign.intervals [[BR]] genome.chr.dbsnpXYZ.rod [[BR]] genome.chr.indelsXYZ.vcf ||
-||outputs: ||sample.chr.realigned.bam ||
-||doc:     ||http://www.broadinstitute.org/gsa/wiki/index.php/Local_realignment_around_indels#Realigning ||
-
-=== !FixMateInformation ===
-See description in workflow2, now applied to sample
-
-||inputs:  ||sample.chr.realigned.bam ||
-||ouputs:  ||sample.chr.matesfixed.bam ||
-=== IndelGenotyperV2 ===
-Call indels
-
-||tool:    ||GenomeAnalysisTK.jar -T IndelGenotyperV2 ||
-||inputs:  ||sample.chr.matesfixed.bam [[BR]]genome.chr.fa ||
-||outputs: ||sample.chr.indels.vcf [[BR]]sample.chr.indels.bed [[BR]]sample.chr.indels.txt ||
-||doc:     ||http://www.broadinstitute.org/gsa/wiki/index.php/Indel_Genotyper_V2.0 [[BR]]
-
-http://www.broadinstitute.org/gsa/wiki/index.php/Firehose_Parameters#SampleIndelGenotyper ||
-=== filterSingleSampleCalls ===
-Filter indels
-
-||tool:    ||filterSingleSampleCalls.pl ||
-||inputs:  ||sample.chr.indels.bed ||
-||outputs: ||sample.chr.indels.filtered.bed ||
-||doc:     ||http://www.broadinstitute.org/gsa/wiki/index.php/Firehose_Parameters#SampleIndelGenotyper ||
-
-=== !UnifiedGenotyper ===
-Call SNPs
-
-||tool:    ||GenomeAnalysisTK.jar -T UnifiedGenotyper ||
-||inputs:  ||sample.chr.matesfixed [[BR]]genome.chr.fa [[BR]]dbsnpXYz.chr.rod ||
-||outputs: ||sample.chr.snps.vcf ||
-||doc:     ||http://www.broadinstitute.org/gsa/wiki/index.php/Firehose_Parameters#SetUnifiedGenotypertoEval [[BR]]
-
-http://www.broadinstitute.org/gsa/wiki/index.php/Unified_genotyper ||
-=== makeIndelMask ===
-Make indel mask
-
-||tool:    ||makeIndelMask.py ||
-||inputs:  ||sample.chr.indels.bed ||
-||outputs: ||sample.chr.indels.mask.bed ||
-||doc:     ||http://www.broadinstitute.org/gsa/wiki/index.php/Indel_Genotyper_V2.0#Creating_a_indel_mask_file ||
-
-=== !VariantFiltration ===
-Filter variants to get the best calls possible
-
-||tool:    ||GenomeAnalysisTK.jar -T VariantFiltration ||
-||inputs:  ||sample.chr.snps.vcf [[BR]]genome.chr.fa [[BR]]dbsnpXYz.chr.rod  ||
-||outputs: ||sample.chr.snps.filtered.vcf ||
-||doc:     ||http://www.broadinstitute.org/gsa/wiki/index.php/Best_Practice_Variant_Detection_with_the_GATK_v2#Integrating_analyses:_getting_the_best_call_set_possible 
-
-||
-
-=== !MergeVcfs ===
-=== !ChipVcf ===
-Produce vcf for the chips
-
-=== !VariantEval ===
-Create summary information on the variations called for evaluation.
-Run per sample.snps.filtered.vcf against chip.
-
-||tool:    ||GenomeAnalysisTK.jar -T VariantEval ||
-||inputs:  ||sample.snps.vcf [[BR]]sample.chip.vcf [[BR]]genome.chr.fa [[BR]]dbsnpXYz.chr.rod||
-||outputs: ||sample.snps.eval ||
-||doc:     ||http://www.broadinstitute.org/gsa/wiki/index.php/VariantEval ||
-
-
-Discussion:
-> Do we call SNPs based on the filtered indels or the raw indels?
-> Should we realign AGAIN after merge of lanes?
-> BAQ?
-> MINDEL/PINDEL?