Changes between Version 40 and Version 41 of SnpCallingPipeline


Ignore:
Timestamp:
Oct 18, 2010 4:41:51 AM (12 years ago)
Author:
Morris Swertz
Comment:

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  • SnpCallingPipeline

    v40 v41  
    88
    99To 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.
     10
     11* SnpCallingPipeline/ReferencePreparation
     12* SnpCallingPipeline/AlignmentAndCleaning
     13* SnpCallingPipeline/VariantCalling
     14
    1015== Simplified Overview ==
    1116
     
    259264> wy do we need to sort and index after recalibration? does it mess up the order of things?
    260265
    261 == Workflow 3: sample level variant calling ==
    262 This workflow will call variants for the samples including:
    263 * sample level recalibration
    264 * sample level realignment
    265 N.B. no sample level MarkDuplicates is needed as lanes == libraries.
    266 
    267 Workflow inputs:
    268 * lane.chr.recal.sorted.bam - for all sample lanes: dedupped, recalibrated, realigned, sorted and indexed bams (3)
    269 * sample.chip.vcf - genotypes called from genotype chip
    270 Reference:
    271 * genome.chr.fasta - reference genome split on chromosome
    272 * genome.chr.realign.intervals - targets for realignment per chromosome
    273 * genome.chr.dbsnpXYZ.rod - known snp variants, here from dpbsnp
    274 * genome.chr.indelsXYZ.vcf - known indels from, here from 1KG
    275 
    276 Workflow outputs:
    277 * sample.chr.bam - merged bam files per sample
    278 * sample.chr.realign.interval - realignment target intervals
    279 * sample.chr.realigned.bam - realigned
    280 * sample.chr.matesfixed.bam - fixed pairs in realignment
    281 * sample.chr.indels.vcf - raw indels called
    282 * sample.chr.indels.bed - raw indels annotations
    283 * sample.chr.indels.txt - output from the indel calling
    284 * sample.chr.indels.filtered.bed - indels filtered
    285 * sample.chr.snps.vcf - raw snps called
    286 * sample.chr.snps.filtered.vcf - snps filtered
    287 
    288 === merge-lanes ===
    289 Merge lanes into one sample bam
    290 
    291 ||tool:    ||sam merge ||
    292 ||inputs:  ||lane.chr.recal.sorted.bam ||
    293 ||outputs: ||sample.chr.bam ||
    294 ||docs:    ||http://samtools.sourceforge.net/samtools.shtml ||
    295 
    296 === !RealignerTargetCreator ===
    297 Create realignment targets based on the data (so not only knowns)
    298 
    299 ||tool:    ||GenomeAnalysisTK.jar -T RealignerTargetCreator ||
    300 ||inputs:  ||sample.chr.bam [[BR]]genome.chr.fa [[BR]]dbsnpXYz.chr.rod [[BR]]indelsXYZ.vcf
    301 ||outputs: ||sample.chr.realign.intervals ||
    302 ||doc:     ||http://www.broadinstitute.org/gsa/wiki/index.php/Local_realignment_around_indels#Creating_Intervals ||
    303 
    304 === !IndelRealigner ===
    305 Realign based on realignment targets in previous step
    306 
    307 ||tool:    ||GenomeAnalysisTK.jar -T IndelRealigner ||
    308 ||inputs:  ||sample.chr.bam [[BR]]genome.chr.realign.intervals [[BR]] genome.chr.dbsnpXYZ.rod [[BR]] genome.chr.indelsXYZ.vcf ||
    309 ||outputs: ||sample.chr.realigned.bam ||
    310 ||doc:     ||http://www.broadinstitute.org/gsa/wiki/index.php/Local_realignment_around_indels#Realigning ||
    311 
    312 === !FixMateInformation ===
    313 See description in workflow2, now applied to sample
    314 
    315 ||inputs:  ||sample.chr.realigned.bam ||
    316 ||ouputs:  ||sample.chr.matesfixed.bam ||
    317 === IndelGenotyperV2 ===
    318 Call indels
    319 
    320 ||tool:    ||GenomeAnalysisTK.jar -T IndelGenotyperV2 ||
    321 ||inputs:  ||sample.chr.matesfixed.bam [[BR]]genome.chr.fa ||
    322 ||outputs: ||sample.chr.indels.vcf [[BR]]sample.chr.indels.bed [[BR]]sample.chr.indels.txt ||
    323 ||doc:     ||http://www.broadinstitute.org/gsa/wiki/index.php/Indel_Genotyper_V2.0 [[BR]]
    324 
    325 http://www.broadinstitute.org/gsa/wiki/index.php/Firehose_Parameters#SampleIndelGenotyper ||
    326 === filterSingleSampleCalls ===
    327 Filter indels
    328 
    329 ||tool:    ||filterSingleSampleCalls.pl ||
    330 ||inputs:  ||sample.chr.indels.bed ||
    331 ||outputs: ||sample.chr.indels.filtered.bed ||
    332 ||doc:     ||http://www.broadinstitute.org/gsa/wiki/index.php/Firehose_Parameters#SampleIndelGenotyper ||
    333 
    334 === !UnifiedGenotyper ===
    335 Call SNPs
    336 
    337 ||tool:    ||GenomeAnalysisTK.jar -T UnifiedGenotyper ||
    338 ||inputs:  ||sample.chr.matesfixed [[BR]]genome.chr.fa [[BR]]dbsnpXYz.chr.rod ||
    339 ||outputs: ||sample.chr.snps.vcf ||
    340 ||doc:     ||http://www.broadinstitute.org/gsa/wiki/index.php/Firehose_Parameters#SetUnifiedGenotypertoEval [[BR]]
    341 
    342 http://www.broadinstitute.org/gsa/wiki/index.php/Unified_genotyper ||
    343 === makeIndelMask ===
    344 Make indel mask
    345 
    346 ||tool:    ||makeIndelMask.py ||
    347 ||inputs:  ||sample.chr.indels.bed ||
    348 ||outputs: ||sample.chr.indels.mask.bed ||
    349 ||doc:     ||http://www.broadinstitute.org/gsa/wiki/index.php/Indel_Genotyper_V2.0#Creating_a_indel_mask_file ||
    350 
    351 === !VariantFiltration ===
    352 Filter variants to get the best calls possible
    353 
    354 ||tool:    ||GenomeAnalysisTK.jar -T VariantFiltration ||
    355 ||inputs:  ||sample.chr.snps.vcf [[BR]]genome.chr.fa [[BR]]dbsnpXYz.chr.rod  ||
    356 ||outputs: ||sample.chr.snps.filtered.vcf ||
    357 ||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
    358 
    359 ||
    360 
    361 === !MergeVcfs ===
    362 === !ChipVcf ===
    363 Produce vcf for the chips
    364 
    365 === !VariantEval ===
    366 Create summary information on the variations called for evaluation.
    367 Run per sample.snps.filtered.vcf against chip.
    368 
    369 ||tool:    ||GenomeAnalysisTK.jar -T VariantEval ||
    370 ||inputs:  ||sample.snps.vcf [[BR]]sample.chip.vcf [[BR]]genome.chr.fa [[BR]]dbsnpXYz.chr.rod||
    371 ||outputs: ||sample.snps.eval ||
    372 ||doc:     ||http://www.broadinstitute.org/gsa/wiki/index.php/VariantEval ||
    373 
    374 
    375 Discussion:
    376 > Do we call SNPs based on the filtered indels or the raw indels?
    377 > Should we realign AGAIN after merge of lanes?
    378 > BAQ?
    379 > MINDEL/PINDEL?