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Tutorial: GotCloud UW CMG (view source)

Revision as of 12:37, 6 August 2013

6,524 bytes added ,  12:37, 6 August 2013
→‎STEP 3 : Run GotCloud SNP Calling Pipeline
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  % ${GC}/gotcloud/gotcloud snpcall --conf ${GC}/examples/index/chr7.CFTR.low_coverage.conf --outDir snps --baseprefix ${GC}/examples --region 7:117000000-117500000 --numjobs 2
 
  % ${GC}/gotcloud/gotcloud snpcall --conf ${GC}/examples/index/chr7.CFTR.low_coverage.conf --outDir snps --baseprefix ${GC}/examples --region 7:117000000-117500000 --numjobs 2
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CHRS = 7
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BAM_INDEX = index/chr7.CFTR.low_coverage.index
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############
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# References
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REF_ROOT = chr7Ref
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#
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REF = $(REF_ROOT)/hs37d5.chr7.fa
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INDEL_PREFIX = $(REF_ROOT)/1kg.pilot_release.merged.indels.sites.hg19
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DBSNP_VCF =  $(REF_ROOT)/dbsnp_135.b37.chr7.CFTR.vcf.gz
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HM3_VCF =  $(REF_ROOT)/hapmap_3.3.b37.sites.chr7.CFTR.vcf.gz
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OMNI_VCF = $(REF_ROOT)/1000G_omni2.5.b37.sites.PASS.chr7.CFTR.vcf.gz
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[presenter02@uwcmg002 test]$ time ${GC}/gotcloud/gotcloud snpcall --conf ${GC}/examples/index/chr7.CFTR.low_coverage.conf --outDir snps --baseprefix ${GC}/examples --region 7:117000000-117500000 --numjobs 2
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Key configurations:
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GOTCLOUD_ROOT: /home/presenter02/day2/session1/uwcmg_2013_08/gotcloud
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OUT_DIR:      snps
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BAM_INDEX:    index/chr7.CFTR.low_coverage.index
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REF:          chr7Ref/hs37d5.chr7.fa
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CHRS:          7
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BATCH_TYPE:    local
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BATCH_OPTS:   
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Processing the following steps...
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2: RUN_PILEUP
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3: RUN_GLFMULTIPLES
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4: RUN_VCFPILEUP
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5: RUN_FILTER
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6: RUN_SVM
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8: RUN_SPLIT
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Call region is 7:117000000-117500000
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Generating commands for chr7...
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Creating glf INDEX at 7:115000001-120000000..
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--------------------------------------------------------------------
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Finished creating makefile /home/presenter02/test/snps/umake.Makefile
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Running /home/presenter02/test/snps/umake.Makefile
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Start merging VCFs...
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Merging /home/presenter02/test/snps/vcfs/chr7/115000001.120000000/chr7.115000001.120000000.vcf into STDOUT...
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Start merging VCFs...
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Merging /home/presenter02/test/snps/vcfs/chr7/115000001.120000000/chr7.115000001.120000000.stats.vcf into STDOUT...
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The following parameters are available.  Ones with "[]" are in effect:
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Available Options
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                          Recipes : --write-bed, --write-vcf [ON], --upgrade,
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                                    --summarize, --filter [ON], --subset
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                VCF Input options : --in-vcf [/home/presenter02/test/snps/vcfs/chr7/chr7.merged.stats.vcf]
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                BED Input options : --in-bfile [], --in-bed [], --in-bim [],
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                                    --in-fam [],
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                                    --ref [/data/local/ref/karma.ref/human.g1k.v37.fa]
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              Subsetting options : --in-subset [], --mono-subset,
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                                    --filt-only-subset
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                  Output Options : --out [/home/presenter02/test/snps/vcfs/chr7/chr7.hardfiltered.sites.vcf],
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                                    --qGeno, --print-every [10000]
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      Output compression Options : --plain [ON], --bgzf, --gzip
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    Genotype-level Filter Options : --minGQ, --minGD
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                  Filter Options : --winIndel [5],
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                                    --indelVCF [/home/presenter02/day2/session1/uwcmg_2013_08/examples/chr7Ref/1kg.pilot_release.merged.indels.sites.hg19.chr7.vcf],
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                                    --minQUAL [5], --minMQ [20],
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                                    --maxDP [99000], --minDP [99],
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                                    --maxABL [70], --winFFRQ, --maxFFRQ,
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                                    --winFVAR, --merFVAR, --maxFVAR,
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                                    --minNS [1], --maxSTP [2147483647],
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                                    --maxTTT [2147483647],
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                                    --minTTT [-2147483648], --maxSTR [20],
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                                    --minSTR [-20], --maxSTZ [5], --minSTZ [-5],
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                                    --maxCBR [20], --minCBR [-100],
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                                    --maxQBR [100], --minQBR [-100],
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                                    --maxCBZ [2147483647], --maxCSR [100],
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                                    --minCSR [-100], --maxLQZ [2147483647],
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                                    --minLQZ [-2147483648],
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                                    --maxRBZ [2147483647],
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                                    --minRBZ [-2147483648],
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                                    --maxIOZ [2147483647],
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                                    --minIOR [-2147483648],
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                                    --maxIOR [2147483647],
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                                    --maxAOZ [2147483647], --maxAOI [5],
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                                    --maxMQ0 [10], --maxMQ10 [100],
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                                    --maxMQ20 [100], --minFIC [-20],
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                                    --minABE [-100], --maxABE [100],
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                                    --maxLQR [30], --minMBR [-100],
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                                    --maxMBR [100], --minABZ [-2147483648],
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                                    --maxABZ [2147483647],
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                                    --maxBCS [2147483647], --keepFilter
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Analysis started on Tue Aug  6 12:25:04 2013
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The following filters are in effect:
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m20 : MQ >= 20.00
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dp99 : DP >= 99.00
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DP99000 : DP <= 99000.00
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ns1 : NS >= 1.00
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AB70 : AB <= 0.70
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STR20 : STR <= 0.20
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str-20 : STR >= -0.20
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stz-5 : STZ >= -5.00
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STZ5 : STZ <= 5.00
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CBR20 : CBR <= 0.20
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AOI5 : AOI <= 5.00
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MQ0_10 : MQ0 <= 0.10
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fic-20 : FIC >= -0.20
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LQR30 : LQR <= 0.30
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q5 : QUAL >= 5
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INDEL5 : INDEL >= 5 bp with /home/presenter02/day2/session1/uwcmg_2013_08/examples/chr7Ref/1kg.pilot_release.merged.indels.sites.hg19.chr7.vcf
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Writing to VCF file /home/presenter02/test/snps/vcfs/chr7/chr7.hardfiltered.sites.vcf
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Analysis finished on Tue Aug  6 12:25:05 2013
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loading /home/presenter02/day2/session1/uwcmg_2013_08/examples/chr7Ref/dbsnp_135.b37.chr7.CFTR.vcf.gz as a VCF input..
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finished loading dbSNP for 7415 variants
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TOTAL 1538 1538 662 378 166 25 145 129 27 6
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The following parameters are available.  Ones with "[]" are in effect:
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Available Options
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                Input options : --in [/home/presenter02/test/snps/vcfs/chr7/chr7.filtered.sites.vcf.raw],
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                                --ignore
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                Output Options : --out [/home/presenter02/test/snps/vcfs/chr7/chr7.filtered.sites.vcf.norm],
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                                --digits [3], --rank, --verbose [ON]
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    Output compression Options : --plain [ON], --bgzf, --gzip
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Analysis started on Tue Aug  6 12:25:05 2013
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Reading Input File /home/presenter02/test/snps/vcfs/chr7/chr7.filtered.sites.vcf.raw
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Finished Reading 1538 lines
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Starting sorting values
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Writing output values
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Analysis finished on Tue Aug  6 12:25:05 2013
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loading /home/presenter02/day2/session1/uwcmg_2013_08/examples/chr7Ref/dbsnp_135.b37.chr7.CFTR.vcf.gz as a VCF input..
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finished loading dbSNP for 7415 variants
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TOTAL 1538 1538 662 378 166 25 145 129 27 6
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  Commands finished in 306 secs with no errors reported
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--------------------------------------------------------------------
    
  % cat ${GC}/out/snps/vcfs/chr7/chr7.filtered.sites.vcf.summary
 
  % cat ${GC}/out/snps/vcfs/chr7/chr7.filtered.sites.vcf.summary
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/7748"

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