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Tutorial: GotCloud UW CMG (view source)

Revision as of 12:09, 6 August 2013

4,607 bytes added ,  12:09, 6 August 2013
→‎Step 1 : GotCloud Alignment Pipeline
Line 32: Line 32:     
  % ls ${GC}/examples/fastq
 
  % ls ${GC}/examples/fastq
 +
SRR035022_1.fastq.gz  SRR035023_1.fastq.gz  SRR035024_1.fastq.gz  SRR035025_1.fastq.gz  SRR035026_1.fastq.gz  SRR035027_1.fastq.gz  SRR035669_1.fastq.gz  SRR622461_1.fastq.gz
 +
SRR035022_2.fastq.gz  SRR035023_2.fastq.gz  SRR035024_2.fastq.gz  SRR035025_2.fastq.gz  SRR035026_2.fastq.gz  SRR035027_2.fastq.gz  SRR035669_2.fastq.gz  SRR622461_2.fastq.gz
 +
SRR035022.fastq.gz    SRR035023.fastq.gz    SRR035024.fastq.gz    SRR035025.fastq.gz    SRR035026.fastq.gz    SRR035027.fastq.gz    SRR035669.fastq.gz    SRR622461.fastq.gz
    
  % ls ${GC}/examples
 
  % ls ${GC}/examples
 +
bams  chr7Ref  fastq  index
    
  % cat ${GC}/examples/index/chr7.CFTR.fastq.index
 
  % cat ${GC}/examples/index/chr7.CFTR.fastq.index
 +
MERGE_NAME FASTQ1 FASTQ2 RGID SAMPLE LIBRARY CENTER PLATFORM
 +
NA06984 fastq/SRR035022.fastq.gz . SRR035022 NA06984 Solexa-16556 BI ILLUMINA
 +
NA06984 fastq/SRR035022_1.fastq.gz fastq/SRR035022_2.fastq.gz SRR035022 NA06984 Solexa-16556 BI ILLUMINA
 +
NA06984 fastq/SRR035023.fastq.gz . SRR035023 NA06984 Solexa-16556 BI ILLUMINA
 +
NA06984 fastq/SRR035023_1.fastq.gz fastq/SRR035023_2.fastq.gz SRR035023 NA06984 Solexa-16556 BI ILLUMINA
 +
NA06984 fastq/SRR035024.fastq.gz . SRR035024 NA06984 Solexa-16556 BI ILLUMINA
 +
NA06984 fastq/SRR035024_1.fastq.gz fastq/SRR035024_2.fastq.gz SRR035024 NA06984 Solexa-16556 BI ILLUMINA
 +
NA06984 fastq/SRR035025.fastq.gz . SRR035025 NA06984 Solexa-16556 BI ILLUMINA
 +
NA06984 fastq/SRR035025_1.fastq.gz fastq/SRR035025_2.fastq.gz SRR035025 NA06984 Solexa-16556 BI ILLUMINA
 +
NA06984 fastq/SRR035026.fastq.gz . SRR035026 NA06984 Solexa-16556 BI ILLUMINA
 +
NA06984 fastq/SRR035026_1.fastq.gz fastq/SRR035026_2.fastq.gz SRR035026 NA06984 Solexa-16556 BI ILLUMINA
 +
NA06984 fastq/SRR035027.fastq.gz . SRR035027 NA06984 Solexa-16556 BI ILLUMINA
 +
NA06984 fastq/SRR035027_1.fastq.gz fastq/SRR035027_2.fastq.gz SRR035027 NA06984 Solexa-16556 BI ILLUMINA
 +
NA06984 fastq/SRR035669.fastq.gz . SRR035669 NA06984 Solexa-16556 BI ILLUMINA
 +
NA06984 fastq/SRR035669_1.fastq.gz fastq/SRR035669_2.fastq.gz SRR035669 NA06984 Solexa-16556 BI ILLUMINA
 +
NA12878 fastq/SRR622461.fastq.gz . SRR622461 NA12878 Illumina_NA12878 ILLUMINA ILLUMINA
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NA12878 fastq/SRR622461_1.fastq.gz fastq/SRR622461_2.fastq.gz SRR622461 NA12878 Illumina_NA12878 ILLUMINA ILLUMINA
    
  % cat ${GC}/examples/index/chr7.CFTR.align.conf
 
  % cat ${GC}/examples/index/chr7.CFTR.align.conf
 +
INDEX_FILE = index/chr7.CFTR.fastq.index
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###################
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# References
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REF_DIR = chr7Ref
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AS = NCBI37
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REF = $(REF_DIR)/hs37d5.chr7.fa
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DBSNP_VCF =  $(REF_DIR)/dbsnp_135.b37.chr7.CFTR.vcf.gz
 +
HM3_VCF = $(REF_DIR)/hapmap_3.3.b37.sites.chr7.CFTR.vcf.gz
    
  % mkdir test
 
  % mkdir test
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  % ${GC}/gotcloud/gotcloud align --conf ${GC}/examples/index/chr7.CFTR.align.conf --outDir align --baseprefix ${GC}/examples
 
  % ${GC}/gotcloud/gotcloud align --conf ${GC}/examples/index/chr7.CFTR.align.conf --outDir align --baseprefix ${GC}/examples
 +
Retrieved 168 bytes.
 +
Random chance is 54  (compared to 30)
 +
File sizes of 32 FASTQ input files referenced in '/home/presenter02/day2/session1/uwcmg_2013_08/examples/index/chr7.CFTR.fastq.index' = 6849341.4
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Size of BAMs from aligner will be about 0.01 GB
 +
Intermediate files from snpcaller will be about 0.01 GB
 +
Final VCF output from snpcaller will be about 0.00 GB
 +
Be sure you have enough space to hold all this data
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Created /home/presenter02/test/align/Makefiles/align_NA06984.Makefile
 +
Created /home/presenter02/test/align/Makefiles/align_NA12878.Makefile
 +
---------------------------------------------------------------------
 +
Waiting while samples are processed...
 +
Processing finished in 42 secs with no errors reported
    
Examine the QC metrics by
 
Examine the QC metrics by
    
  % ls align/bams
 
  % ls align/bams
 +
NA06984.recal.bam      NA06984.recal.bam.bai.done  NA06984.recal.bam.metrics  NA12878.recal.bam      NA12878.recal.bam.bai.done  NA12878.recal.bam.metrics
 +
NA06984.recal.bam.bai  NA06984.recal.bam.done      NA06984.recal.bam.qemp    NA12878.recal.bam.bai  NA12878.recal.bam.done      NA12878.recal.bam.qemp
 
   
 
   
 
  % ls align/QCFiles
 
  % ls align/QCFiles
 +
NA06984.genoCheck.depthRG  NA06984.genoCheck.selfRG  NA06984.qplot.R            NA12878.genoCheck.depthSM  NA12878.genoCheck.selfSM  NA12878.qplot.stats
 +
NA06984.genoCheck.depthSM  NA06984.genoCheck.selfSM  NA06984.qplot.stats        NA12878.genoCheck.done    NA12878.qplot.done
 +
NA06984.genoCheck.done    NA06984.qplot.done        NA12878.genoCheck.depthRG  NA12878.genoCheck.selfRG  NA12878.qplot.R
    
  % cat align/QCFiles/NA06984.qplot.stats
 
  % cat align/QCFiles/NA06984.qplot.stats
 +
Stats\BAM /home/presenter02/test2/align/bams/NA06984.recal.bam
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TotalReads(e6) 0.06
 +
MappingRate(%) 97.44
 +
MapRate_MQpass(%) 97.44
 +
TargetMapping(%) 0.00
 +
ZeroMapQual(%) 0.56
 +
MapQual<10(%) 0.70
 +
PairedReads(%) 98.27
 +
ProperPaired(%) 92.83
 +
MappedBases(e9) 0.00
 +
Q20Bases(e9) 0.00
 +
Q20BasesPct(%) 95.27
 +
MeanDepth 7.33
 +
GenomeCover(%) 0.33
 +
EPS_MSE 293.97
 +
EPS_Cycle_Mean 25.06
 +
GCBiasMSE 0.00
 +
ISize_mode 335
 +
ISize_medium 331
 +
DupRate(%) 2.05
 +
QCFailRate(%) 0.00
 +
BaseComp_A(%) 31.8
 +
BaseComp_C(%) 18.4
 +
BaseComp_G(%) 18.1
 +
BaseComp_T(%) 31.6
 +
BaseComp_O(%) 0.0
    
  % cat align/QCFiles/NA06984.genoCheck.selfSM
 
  % cat align/QCFiles/NA06984.genoCheck.selfSM
 +
#SEQ_ID RG CHIP_ID #SNPS #READS AVG_DP FREEMIX FREELK1 FREELK0 FREE_RH FREE_RA CHIPMIX CHIPLK1 CHIPLK0 CHIP_RH CHIP_RA DPREF RDPHET RDPALT
 +
NA06984 ALL NA 175 1038 5.93 0.00841 351.80 351.85 NA NA NA NA NA NA NA NA NA NA
    
== STEP 3 : Run GotCloud SNP Calling Pipeline ==  
 
== STEP 3 : Run GotCloud SNP Calling Pipeline ==  
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/7743"

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