Changes between Initial Version and Version 1 of SnpCallingPipeline/VariantCalling


Ignore:
Timestamp:
Oct 18, 2010 4:42:50 AM (14 years ago)
Author:
Morris Swertz
Comment:

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  • SnpCallingPipeline/VariantCalling

    v1 v1  
     1= Workflow 3: sample level variant calling =
     2[[TOC()]]
     3
     4This workflow will call variants for the samples including:
     5* sample level recalibration
     6* sample level realignment
     7N.B. no sample level MarkDuplicates is needed as lanes = libraries.
     8
     9Workflow inputs:
     10* lane.chr.recal.sorted.bam - for all sample lanes: dedupped, recalibrated, realigned, sorted and indexed bams (3)
     11* sample.chip.vcf - genotypes called from genotype chip
     12Reference:
     13* genome.chr.fasta - reference genome split on chromosome
     14* genome.chr.realign.intervals - targets for realignment per chromosome
     15* genome.chr.dbsnpXYZ.rod - known snp variants, here from dpbsnp
     16* genome.chr.indelsXYZ.vcf - known indels from, here from 1KG
     17
     18Workflow outputs:
     19* sample.chr.bam - merged bam files per sample
     20* sample.chr.realign.interval - realignment target intervals
     21* sample.chr.realigned.bam - realigned
     22* sample.chr.matesfixed.bam - fixed pairs in realignment
     23* sample.chr.indels.vcf - raw indels called
     24* sample.chr.indels.bed - raw indels annotations
     25* sample.chr.indels.txt - output from the indel calling
     26* sample.chr.indels.filtered.bed - indels filtered
     27* sample.chr.snps.vcf - raw snps called
     28* sample.chr.snps.filtered.vcf - snps filtered
     29
     30== merge-lanes ==
     31Merge lanes into one sample bam
     32
     33||tool:    ||sam merge ||
     34||inputs:  ||lane.chr.recal.sorted.bam ||
     35||outputs: ||sample.chr.bam ||
     36||docs:    ||http://samtools.sourceforge.net/samtools.shtml ||
     37
     38== !RealignerTargetCreator ==
     39Create realignment targets based on the data (so not only knowns)
     40
     41||tool:    ||GenomeAnalysisTK.jar -T RealignerTargetCreator ||
     42||inputs:  ||sample.chr.bam [[BR]]genome.chr.fa [[BR]]dbsnpXYz.chr.rod [[BR]]indelsXYZ.vcf
     43||outputs: ||sample.chr.realign.intervals ||
     44||doc:     ||http://www.broadinstitute.org/gsa/wiki/index.php/Local_realignment_around_indels#Creating_Intervals ||
     45
     46== !IndelRealigner ==
     47Realign based on realignment targets in previous step
     48
     49||tool:    ||GenomeAnalysisTK.jar -T IndelRealigner ||
     50||inputs:  ||sample.chr.bam [[BR]]genome.chr.realign.intervals [[BR]] genome.chr.dbsnpXYZ.rod [[BR]] genome.chr.indelsXYZ.vcf ||
     51||outputs: ||sample.chr.realigned.bam ||
     52||doc:     ||http://www.broadinstitute.org/gsa/wiki/index.php/Local_realignment_around_indels#Realigning ||
     53
     54== !FixMateInformation ==
     55See description in workflow2, now applied to sample
     56
     57||inputs:  ||sample.chr.realigned.bam ||
     58||ouputs:  ||sample.chr.matesfixed.bam ||
     59== IndelGenotyperV2 ==
     60Call indels
     61
     62||tool:    ||GenomeAnalysisTK.jar -T IndelGenotyperV2 ||
     63||inputs:  ||sample.chr.matesfixed.bam [[BR]]genome.chr.fa ||
     64||outputs: ||sample.chr.indels.vcf [[BR]]sample.chr.indels.bed [[BR]]sample.chr.indels.txt ||
     65||doc:     ||http://www.broadinstitute.org/gsa/wiki/index.php/Indel_Genotyper_V2.0 [[BR]]
     66
     67http://www.broadinstitute.org/gsa/wiki/index.php/Firehose_Parameters#SampleIndelGenotyper ||
     68== filterSingleSampleCalls ==
     69Filter indels
     70
     71||tool:    ||filterSingleSampleCalls.pl ||
     72||inputs:  ||sample.chr.indels.bed ||
     73||outputs: ||sample.chr.indels.filtered.bed ||
     74||doc:     ||http://www.broadinstitute.org/gsa/wiki/index.php/Firehose_Parameters#SampleIndelGenotyper ||
     75
     76== !UnifiedGenotyper ==
     77Call SNPs
     78
     79||tool:    ||GenomeAnalysisTK.jar -T UnifiedGenotyper ||
     80||inputs:  ||sample.chr.matesfixed [[BR]]genome.chr.fa [[BR]]dbsnpXYz.chr.rod ||
     81||outputs: ||sample.chr.snps.vcf ||
     82||doc:     ||http://www.broadinstitute.org/gsa/wiki/index.php/Firehose_Parameters#SetUnifiedGenotypertoEval [[BR]]
     83
     84http://www.broadinstitute.org/gsa/wiki/index.php/Unified_genotyper ||
     85== makeIndelMask ==
     86Make indel mask
     87
     88||tool:    ||makeIndelMask.py ||
     89||inputs:  ||sample.chr.indels.bed ||
     90||outputs: ||sample.chr.indels.mask.bed ||
     91||doc:     ||http://www.broadinstitute.org/gsa/wiki/index.php/Indel_Genotyper_V2.0#Creating_a_indel_mask_file ||
     92
     93== !VariantFiltration ==
     94Filter variants to get the best calls possible
     95
     96||tool:    ||GenomeAnalysisTK.jar -T VariantFiltration ||
     97||inputs:  ||sample.chr.snps.vcf [[BR]]genome.chr.fa [[BR]]dbsnpXYz.chr.rod  ||
     98||outputs: ||sample.chr.snps.filtered.vcf ||
     99||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
     100
     101||
     102
     103== !MergeVcfs ==
     104== !ChipVcf ==
     105Produce vcf for the chips
     106
     107== !VariantEval ==
     108Create summary information on the variations called for evaluation.
     109Run per sample.snps.filtered.vcf against chip.
     110
     111||tool:    ||GenomeAnalysisTK.jar -T VariantEval ||
     112||inputs:  ||sample.snps.vcf [[BR]]sample.chip.vcf [[BR]]genome.chr.fa [[BR]]dbsnpXYz.chr.rod||
     113||outputs: ||sample.snps.eval ||
     114||doc:     ||http://www.broadinstitute.org/gsa/wiki/index.php/VariantEval ||
     115
     116
     117Discussion:
     118> Do we call SNPs based on the filtered indels or the raw indels?
     119> Should we realign AGAIN after merge of lanes?
     120> BAQ?
     121> MINDEL/PINDEL?