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 |
| + | 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 |
| + | ################### |
| + | # References |
| + | REF_DIR = chr7Ref |
| + | AS = NCBI37 |
| + | REF = $(REF_DIR)/hs37d5.chr7.fa |
| + | 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 |
Line 46: |
Line 75: |
| | | |
| % ${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 |
| + | 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 |
| + | 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 |
| + | 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 == |