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| Name | Modified | Size | Downloads / Week |
|---|---|---|---|
| Parent folder | |||
| P0667N_GATKrealigned_duplicates_marked.bam | 2012-05-30 | 566.5 MB | |
| P0667T_GATKrealigned_duplicates_marked.bam | 2012-05-30 | 535.6 MB | |
| README.txt | 2012-05-30 | 2.5 kB | |
| P0667T_GATKrealigned_duplicates_marked.bam.bai | 2012-05-30 | 5.7 MB | |
| P0667N_GATKrealigned_duplicates_marked.bam.bai | 2012-05-30 | 5.8 MB | |
| 0247401_D_BED_20090724_hg19_MERGED.bed | 2012-05-30 | 250.9 kB | |
| Totals: 6 Items | 1.1 GB | 0 | |
- Reference file: human_g1k_v37.fasta (1000 genomes version of HG19) - BED and BAM files as follows. (bai files not required) [lij@pmc-bioinf02 test_bams]$ ls 0247401_D_BED_20090724_hg19_MERGED.bed P0667N_GATKrealigned_duplicates_marked.bam.bai P0667T_GATKrealigned_duplicates_marked.bam.bai P0667N_GATKrealigned_duplicates_marked.bam P0667T_GATKrealigned_duplicates_marked.bam [lij@pmc-bioinf02 test_bams]$ ~/me/CONTRA.v2.0.2/contra.py -t 0247401_D_BED_20090724_hg19_MERGED.bed -s P0667T_GATKrealigned_duplicates_marked.bam -c P0667N_GATKrealigned_duplica tes_marked.bam -f $HumanREF -o P0667Test target : 0247401_D_BED_20090724_hg19_MERGED.bed test : P0667T_GATKrealigned_duplicates_marked.bam control : P0667N_GATKrealigned_duplicates_marked.bam fasta : /mnt/Storage/NextGenSequencing/ReferenceFiles/Genomes/HG19/human_g1k_v37.fasta outfolder : P0667Test numBin : [20] minreaddepth : 10 minNBases : 10 sam : False pval : 0.05 sampleName : No-SampleName nomultimapped : False plot : False bedInput : False minExon : 2000 largeDeletion : False Creating Output Folder : Done. Converting TEST Sample... Converting CONTROL Sample... Getting targeted regions DOC... chr1 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 Getting targeted regions DOC... chr1 chr18 chr19 chr2 chr20 chr21 chr22 chr3 chr4 chr5 chr10 chr11 chr6 chr12 chr13 chr7 chr8 chr14 chr15 chr9 chrX chr16 chr17 chr18 chr19 Targeted regions pre-processing: Done chr2 chr20 chr21 chr22 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chrX Targeted regions pre-processing: Done Test file read depth = 337238927 Control file read depth = 304812391 Pre-processing Completed. Getting the Log Ratio ... Binning ... End of assign.bin.number.py with 11620 exons in 3 bins Significance Test ... [1] "P0667Test/buf/bin20.txt" [1] "End of cn_analysis.R" [1] 11616 Generating Output Files ... Creating VCF file ... P0667Test/table/CNATable.10rd.10bases.20bins.vcf created. Temp Folder Removed Done... [lij@pmc-bioinf02 test_bams]$ ls 0247401_D_BED_20090724_hg19_MERGED.bed P0667N_GATKrealigned_duplicates_marked.bam.bai P0667T_GATKrealigned_duplicates_marked.bam P0667N_GATKrealigned_duplicates_marked.bam P0667Test P0667T_GATKrealigned_duplicates_marked.bam.bai [lij@pmc-bioinf02 test_bams]$
