Changes between Version 41 and Version 42 of SnpCallingPipeline


Ignore:
Timestamp:
Oct 18, 2010 4:43:35 AM (12 years ago)
Author:
Morris Swertz
Comment:

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  • SnpCallingPipeline

    v41 v42  
    140140||doc:    ||http://www.broadinstitute.org/gsa/wiki/index.php/Local_realignment_around_indels#Running_the_Indel_Realigner_only_at_known_sites ||
    141141
    142 == Workflow 2: Alignment per Lane, per Chr ==
    143142
    144 This workflow aligns reads per lane and chromosome, including:
    145 * re-alignment to prevend false SNP calls caused by indels (using known indels)
    146 * markduplicates to prevend false coverage caused by PCR errors (per library = lane)
    147 * base quality recalibration to correct for false low scores caused by true variation
    148 
    149 Workflow Inputs:
    150 * lane.1.fq.gz - raw reads for lane, pair end 1
    151 * lane.2.fq.gz - raw reads for lane, pair end 2
    152 * genome.chr.fasta - reference genome split on chromosome
    153 * genome.chr.realign.intervals - targets for realignment per chromosome
    154 * genome.chr.dbsnpXYZ.rod - known snp variants, here from dpbsnp
    155 * genome.chr.indelsXYZ.vcf - known indels from, here from 1KG
    156 
    157 Workflow ouputs:
    158 * lane.chr.1.sai - alignment index for first pair
    159 * lane.chr.2.sai - alignment index for second pair
    160 * lane.chr.sam - alignment map for
    161 * lane.chr.bam - alignment map in binary format
    162 * lane.chr.sorted.bam - sorted alignment map
    163 * lane.chr.sorted.bai - sorted alignment index
    164 * lane.chr.dedup.bam - marked duplicate PCR elements
    165 * lane.chr.dedup.metrics - metrics describing deduplication
    166 * lane.chr.realigned.bam - realigned based on known indels
    167 * lane.chr.matefixed.bam - fixed the mate pair ends
    168 * lane.chr.covariate_table.csv - table of countcovariates output for recalibration
    169 * lane.chr.recal.bam - alignment map with recalibrated quality scores
    170 
    171 === align ===
    172 Align each end of paired end.
    173  
    174 ||tool:   ||bwa-align ||
    175 ||input:  ||chr.fasta, lane.1.fq.gz, lane.2.fq.gz ||
    176 ||output: ||lane.chr.1.sai, lane.chr.2.sai ||
    177 ||docs:   ||http://bio-bwa.sourceforge.net/bwa.shtml ||
    178 
    179 === align-pe ===
    180 Align the pairs as one
    181 
    182 ||tool:    ||bwa sampe ||
    183 ||inputs:  ||chr.fasta [[BR]] lane.1.fq.gz [[BR]] lane.2.fq.gz [[BR]] lane.chr.1.sai [[BR]] lane.chr.2.sai ||
    184 ||outputs: ||lane.chr.sam ||
    185 ||docs:    ||http://bio-bwa.sourceforge.net/bwa.shtml ||
    186 
    187 === sam-to-bam ===
    188 Convert sam to bam
    189 
    190 ||tool:    ||samtools view ||
    191 ||inputs:  ||lane.chr.sam ||
    192 ||outputs: ||lane.chr.bam ||
    193 ||docs:    ||http://samtools.sourceforge.net/samtools.shtml ||
    194 
    195 (Question: can this not index and sort?)
    196 
    197 === sam-sort ===
    198 Sort bam file on coordinate
    199 
    200 ||tool:    ||samtools sort ||
    201 ||inputs:  ||lane.chr.bam ||
    202 ||outputs: ||lane.chr.sorted.bam ||
    203 ||docs:    ||http://samtools.sourceforge.net/samtools.shtml ||
    204 
    205 === sam-index ===
    206 Index bam file for quicker access
    207 
    208 ||tool:    ||samtools index ||
    209 ||inputs:  ||lane.chr.sorted.bam ||
    210 ||outputs: ||lane.chr.sorted.bai ||
    211 ||docs:    ||http://samtools.sourceforge.net/samtools.shtml ||
    212 
    213 === !MarkDuplicates ===
    214 Mark duplicate PCR fragments to be filtered in analysis
    215 
    216 ||tool:    ||MarkDuplicates.jar ||
    217 ||inputs:  ||lane.chr.sorted.bam ||
    218 ||outputs: ||lane.chr.dedup.bam [[BR]] lane.chr.dedup.metrics ||
    219 ||docs:    ||http://picard.sourceforge.net/command-line-overview.shtml#MarkDuplicates ||
    220 
    221 === !IndelRealigner-!KnownsOnly ===
    222 Improve the alignment using known indel information (will reduce false SNP calls)
    223 
    224 ||tool:    ||GenomeAnalysisTK.jar -T IndelRealigner ||
    225 ||inputs:  ||lane.chr.dedup.bam [[BR]] genome.chr.realign.intervals [[BR]] genome.chr.dbsnpXYZ.rod [[BR]] genome.chr.indelsXYZ.vcf ||
    226 ||outputs: ||lane.chr.realigned.bam ||
    227 ||docs     ||http://www.broadinstitute.org/gsa/wiki/index.php/Local_realignment_around_indels#Running_the_Indel_Realigner_only_at_known_sites ||
    228 
    229 === !FixMateInformation ===
    230 Fix the paired end information as consequence of the realignment.
    231 
    232 ||tool:    ||FixMateInformation.jar ||
    233 ||inputs:  ||lane.chr.realigned.bam
    234 ||outputs: ||lane.chr.matefixed.bam ||
    235 ||docs:    ||http://picard.sourceforge.net/command-line-overview.shtml#FixMateInformation,
    236 
    237 http://www.broadinstitute.org/gsa/wiki/index.php/Local_realignment_around_indels#Fixing_Mate_Pairs ||
    238 
    239 === !CountCovariates ===
    240 Count covariants, such as machine cycle and bp position, to be used as basis for quality recalibration.
    241 Optionally: plot the results to pdf using AnalyzeCovariates
    242 
    243 ||tool:    ||GenomeAnalysisTK.jar -T CountCovariates, AnalyzeCovariates.jar ||
    244 ||inputs:  ||lane.chr.matefixed.bam [[BR]] genome.chr.dbsnpXYZ.rod ||
    245 ||outputs: ||lane.chr.covariate_table.csv ||
    246 ||docs:    ||http://www.broadinstitute.org/gsa/wiki/index.php/Base_quality_score_recalibration#CountCovariates [[BR]]
    247 
    248 http://www.broadinstitute.org/gsa/wiki/index.php/Base_quality_score_recalibration#AnalyzeCovariates.jar ||
    249 
    250 === !TableRecalibration ===
    251 Recalibrate quality scores based on the covariate table
    252 ||tool:    ||GenomeAnalysisTK.jar -T TableRecalibration ||
    253 ||inputs:  ||lane.chr.matefixed.bam [[BR]]lanec.chr.recal_table.csv [[BR]]chr.fasta ||
    254 ||outputs: ||lane.chr.recal.bam
    255 ||docs:    ||http://www.broadinstitute.org/gsa/wiki/index.php/Base_quality_score_recalibration#TableRecalibration ||
    256 
    257 === Repeat: sam-sort, sam-index, countcovariates ===
    258 See steps above for commands and docs.
    259 
    260 ||inputs:  ||lane.chr.recal.bam ||
    261 ||outputs: ||lane.chr.recal.sorted.bam, lane.chr.recal.sorted.bam.bai, lane.chr.recal.covariate_table.csv ||
    262 
    263 Discussion:
    264 > wy do we need to sort and index after recalibration? does it mess up the order of things?
    265