User:Lindenb/Notebook/UMR915/2012/03/05

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Transfert BAM to server:

XXXX1.fastq.gz                                                                                                           100%   58GB  32.6MB/s   30:29    
XXXX2.fastq.gz                                                                                                           100%   58GB  32.7MB/s   30:21    
XXXXsorted.bam                                                                                                           100%   97GB  30.8MB/s   53:36    
XXXXsorted.bam.bai                                                                                                       100% 8595KB   8.4MB/s   00:01    
XXXX1.fastq.gz                                                                                                           100%   53GB  28.8MB/s   31:36    
XXXX2.fastq.gz                                                                                                           100%   53GB  33.1MB/s   27:29    
XXXXsorted.bam                                                                                                           100%   78GB  33.1MB/s   40:21    
XXXXsorted.bam.bai                                                                                                       100% 8565KB   8.4MB/s   00:01    
XXXX1.fastq.gz                                                                                                           100%   51GB  33.0MB/s   26:34    
XXXX2.fastq.gz                                                                                                           100%   51GB  33.1MB/s   26:22    
XXXXsorted.bam                                                                                                           100%   80GB  33.1MB/s   41:13    
XXXXsorted.bam.bai                                                                                                       100% 8608KB   8.4MB/s   00:00    
XXXX1.fastq.gz                                                                                                           100%   52GB  33.1MB/s   26:37    
XXXX2.fastq.gz                                                                                                           100%   52GB  33.1MB/s   26:37    
XXXXsorted.bam                                                                                                           100%   83GB  33.1MB/s   42:49    
XXXXsorted.bam.bai                                                                                                       100% 8607KB   8.4MB/s   00:00    
XXXX1.fastq.gz                                                                                                            100%   57GB  33.1MB/s   29:34    
XXXX2.fastq.gz                                                                                                            100%   57GB  33.1MB/s   29:38    
XXXXsorted.bam                                                                                                            100%   92GB  33.1MB/s   47:34    
XXXXsorted.bam.bai                                                                                                        100% 8619KB   8.4MB/s   00:00    

Test mpileup

$ samtools mpileup  -D -u  -f hg19.fa DataHD20120302/*/*.bam | bcftools view -bvcg - | bcftools view - | grep -v "##" | head -n 3 | verticalize 
[mpileup] 5 samples in 5 input files
<mpileup> Set max per-file depth to 1600
>>>	2
$1	#CHROM                                 	chr1
$2	POS                                    	9997
$3	ID                                     	.
$4	REF                                    	N
$5	ALT                                    	A
$6	QUAL                                   	3.55
$7	FILTER                                 	.
$8	INFO                                   	DP=1;AF1=1;AC1=10;DP4=0,0,1,0;MQ=60;FQ=-25.5
$9	FORMAT                                 	GT:PL:DP:GQ
$10	DataHD20120302/CD5121/CD5121_sorted.bam	0/1:31,3,0:1:5
$11	DataHD20120302/CD8260/CD8260_sorted.bam	0/0:0,0,0:0:3
$12	DataHD20120302/CD8262/CD8262_sorted.bam	0/0:0,0,0:0:3
$13	DataHD20120302/CD8289/CD8289_sorted.bam	0/0:0,0,0:0:3
$14	DataHD20120302/S0529/S0529_sorted.bam  	0/0:0,0,0:0:3
<<<	2

>>>	3
$1	#CHROM                                 	chr1
$2	POS                                    	9998
$3	ID                                     	.
$4	REF                                    	N
$5	ALT                                    	C
$6	QUAL                                   	29
$7	FILTER                                 	.
$8	INFO                                   	DP=2;AF1=1;AC1=10;DP4=0,0,2,0;MQ=60;FQ=-27.4
$9	FORMAT                                 	GT:PL:DP:GQ
$10	DataHD20120302/CD5121/CD5121_sorted.bam	1/1:31,3,0:1:6
$11	DataHD20120302/CD8260/CD8260_sorted.bam	1/1:0,0,0:0:3
$12	DataHD20120302/CD8262/CD8262_sorted.bam	1/1:0,0,0:0:3
$13	DataHD20120302/CD8289/CD8289_sorted.bam	1/1:0,0,0:0:3
$14	DataHD20120302/S0529/S0529_sorted.bam  	1/1:31,3,0:1:6
<<<	3

vs only one sample:

$ samtools mpileup  -D -u  -f hg19.fa DataHD20120302/CD5121/CD5121_sorted.bam | bcftools view -bvcg - | bcftools view - | grep -v "##" | head -n 3 | verticalize 
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
>>>	2
$1	#CHROM                                 	chr1
$2	POS                                    	9997
$3	ID                                     	.
$4	REF                                    	N
$5	ALT                                    	A
$6	QUAL                                   	3.55
$7	FILTER                                 	.
$8	INFO                                   	DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=60;FQ=-30
$9	FORMAT                                 	GT:PL:DP:GQ
$10	DataHD20120302/CD5121/CD5121_sorted.bam	0/1:31,3,0:1:4
<<<	2

>>>	3
$1	#CHROM                                 	chr1
$2	POS                                    	9998
$3	ID                                     	.
$4	REF                                    	N
$5	ALT                                    	C
$6	QUAL                                   	3.55
$7	FILTER                                 	.
$8	INFO                                   	DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=60;FQ=-30
$9	FORMAT                                 	GT:PL:DP:GQ
$10	DataHD20120302/CD5121/CD5121_sorted.bam	0/1:31,3,0:1:4
<<<	3

exomeCNV

received message from author

"Thank you for your email. I fixed the problem and the script should be functional now. Please let me know if you notice anything else not working or if you have any question about ExomeCNV."


TODO: add the path to samtools in the exomeCNV tools.

updated GATK

$ java -jar /usr/local/package/gatk/GenomeAnalysisTK-1.4-37-g0b29d54/GenomeAnalysisTK.jar -T DepthOfCoverage -omitBaseOutput -omitLocusTable -R /GENOTYPAGE/data/pubdb/ucsc/hg19/chromosomes/hg19.fa -I _jeter.bam -L PCCR.hg19.bed -o _jeter.coverage
INFO  15:46:02,567 RodBindingArgumentTypeDescriptor - Dynamically determined type of PCCR.hg19.bed to be BED 
INFO  15:46:02,604 HelpFormatter - --------------------------------------------------------------------------------- 
INFO  15:46:02,604 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.4-37-g0b29d54, Compiled 2012/02/27 19:56:39 
INFO  15:46:02,605 HelpFormatter - Copyright (c) 2010 The Broad Institute 
INFO  15:46:02,605 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki 
INFO  15:46:02,605 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa 
INFO  15:46:02,606 HelpFormatter - Program Args: -T DepthOfCoverage -omitBaseOutput -omitLocusTable -R /GENOTYPAGE/data/pubdb/ucsc/hg19/chromosomes/hg19.fa -I _jeter.bam -L PCCR.hg19.bed -o _jeter.coverage 
INFO  15:46:02,606 HelpFormatter - Date/Time: 2012/03/05 15:46:02 
INFO  15:46:02,606 HelpFormatter - --------------------------------------------------------------------------------- 
INFO  15:46:02,607 HelpFormatter - --------------------------------------------------------------------------------- 
INFO  15:46:02,624 GenomeAnalysisEngine - Strictness is SILENT 
INFO  15:46:02,675 SAMDataSource$SAMReaders - Initializing SAMRecords in serial 
INFO  15:46:02,693 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02 
INFO  15:46:04,550 DepthOfCoverageWalker - Per-Locus Depth of Coverage output was omitted 
INFO  15:46:04,799 TraversalEngine - [INITIALIZATION COMPLETE; TRAVERSAL STARTING] 
INFO  15:46:04,799 TraversalEngine -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining 
INFO  15:46:34,838 TraversalEngine -   chr1:12953045        2.30e+06   30.3 s       13.2 s      0.9%        55.3 m    54.8 m 
INFO  15:47:04,826 TraversalEngine -   chr1:22902927        3.82e+06   60.3 s       15.8 s      1.6%        63.5 m    62.5 m 
INFO  15:47:34,906 TraversalEngine -   chr1:38006313        5.82e+06   90.4 s       15.5 s      2.5%        59.5 m    57.9 m 
INFO  15:48:04,919 TraversalEngine -   chr1:50310781        7.74e+06    2.0 m       15.6 s      3.3%        60.7 m    58.7 m 
INFO  15:48:34,943 TraversalEngine -   chr1:74940943        8.77e+06    2.5 m       17.1 s      4.0%        63.0 m    60.5 m 
INFO  15:49:04,949 TraversalEngine -   chr1:95363394        9.61e+06    3.0 m       18.8 s      4.5%        66.2 m    63.2 m 
INFO  15:49:35,001 TraversalEngine -  chr1:114133136        1.07e+07    3.5 m       19.7 s      5.1%        68.9 m    65.4 m 
INFO  15:50:05,230 TraversalEngine -  chr1:145293475        1.15e+07    4.0 m       21.0 s      5.5%        73.1 m    69.0 m 
INFO  15:50:35,254 TraversalEngine -  chr1:148756537        1.22e+07    4.5 m       22.1 s      5.7%        78.7 m    74.1 m 
INFO  15:51:05,429 TraversalEngine -  chr1:152382718        1.31e+07    5.0 m       22.9 s      6.1%        81.9 m    76.9 m 
INFO  15:51:35,432 TraversalEngine -  chr1:159557688        1.53e+07    5.5 m       21.7 s      6.9%        79.9 m    74.4 m 
INFO  15:52:05,535 TraversalEngine -  chr1:174957825        1.64e+07    6.0 m       22.0 s      7.6%        79.6 m    73.6 m 
INFO  15:52:35,564 TraversalEngine -  chr1:197112474        1.75e+07    6.5 m       22.4 s      8.2%        79.7 m    73.2 m 
INFO  15:53:05,669 TraversalEngine -  chr1:212241541        1.89e+07    7.0 m       22.3 s      8.9%        78.7 m    71.7 m 
INFO  15:53:35,779 TraversalEngine -  chr1:232650196        2.02e+07    7.5 m       22.4 s      9.7%        77.8 m    70.3 m 
INFO  15:54:05,817 TraversalEngine -  chr1:248512195        2.08e+07    8.0 m       23.1 s     10.2%        78.8 m    70.8 m 
INFO  15:54:35,820 TraversalEngine -   chr2:26541793        2.18e+07    8.5 m       23.4 s     10.8%        78.7 m    70.2 m 
INFO  15:55:05,939 TraversalEngine -   chr2:42979334        2.34e+07    9.0 m       23.2 s     11.5%        78.4 m    69.4 m 
INFO  15:55:35,999 TraversalEngine -   chr2:69098212        2.43e+07    9.5 m       23.5 s     12.1%        78.5 m    69.0 m 
INFO  15:56:06,064 TraversalEngine -   chr2:87420612        2.56e+07   10.0 m       23.5 s     12.8%        78.5 m    68.5 m 
INFO  15:56:36,166 TraversalEngine -  chr2:102501806        2.66e+07   10.5 m       23.8 s     13.3%        79.4 m    68.9 m 
INFO  15:57:06,795 TraversalEngine -  chr2:113147040        2.71e+07   11.0 m       24.4 s     13.6%        81.3 m    70.3 m 
INFO  15:57:36,818 TraversalEngine -  chr2:135965129        2.80e+07   11.5 m       24.7 s     14.1%        81.8 m    70.2 m 
INFO  15:58:06,997 TraversalEngine -  chr2:162226669        2.87e+07   12.0 m       25.1 s     14.6%        82.4 m    70.4 m 
INFO  15:58:37,012 TraversalEngine -  chr2:178364420        2.96e+07   12.5 m       25.4 s     15.2%        82.6 m    70.0 m 
INFO  15:59:07,028 TraversalEngine -  chr2:179621063        3.09e+07   13.0 m       25.3 s     15.5%        84.3 m    71.3 m 
INFO  15:59:37,041 TraversalEngine -  chr2:201534345        3.19e+07   13.5 m       25.5 s     16.0%        84.5 m    71.0 m 
INFO  16:00:07,080 TraversalEngine -  chr2:216299504        3.27e+07   14.0 m       25.7 s     16.5%        84.9 m    70.8 m 
INFO  16:00:37,101 TraversalEngine -  chr2:234181617        3.47e+07   14.5 m       25.2 s     17.3%        83.9 m    69.4 m 
INFO  16:01:07,160 TraversalEngine -   chr3:11851189        3.61e+07   15.0 m       25.0 s     18.1%        83.0 m    68.0 m 
INFO  16:01:37,222 TraversalEngine -   chr3:38607966        3.72e+07   15.5 m       25.1 s     18.8%        82.8 m    67.2 m 
INFO  16:02:07,274 TraversalEngine -   chr3:49201365        3.95e+07   16.0 m       24.4 s     19.6%        82.0 m    65.9 m 
INFO  16:02:37,347 TraversalEngine -   chr3:63638404        4.18e+07   16.5 m       23.8 s     20.4%        81.1 m    64.6 m 
INFO  16:03:07,389 TraversalEngine -  chr3:107778305        4.24e+07   17.0 m       24.1 s     20.9%        81.6 m    64.6 m 
INFO  16:03:37,411 TraversalEngine -  chr3:124437796        4.32e+07   17.5 m       24.4 s     21.5%        81.7 m    64.2 m 
INFO  16:04:07,468 TraversalEngine -  chr3:142525004        4.43e+07   18.0 m       24.4 s     22.2%        81.4 m    63.4 m 
INFO  16:04:37,947 TraversalEngine -  chr3:172163093        4.51e+07   18.6 m       24.7 s     22.7%        81.6 m    63.1 m 
INFO  16:05:08,080 TraversalEngine -  chr3:195511758        4.64e+07   19.1 m       24.6 s     23.4%        81.5 m    62.4 m 
INFO  16:05:38,311 TraversalEngine -    chr4:9401016        4.76e+07   19.6 m       24.7 s     24.1%        81.3 m    61.7 m 
INFO  16:06:08,424 TraversalEngine -   chr4:44691249        4.83e+07   20.1 m       24.9 s     24.6%        81.5 m    61.5 m 
INFO  16:06:38,570 TraversalEngine -   chr4:73968224        4.91e+07   20.6 m       25.1 s     25.1%        81.8 m    61.2 m 
INFO  16:07:08,644 TraversalEngine -   chr4:95561441        4.99e+07   21.1 m       25.4 s     25.7%        81.9 m    60.9 m 
INFO  16:07:38,669 TraversalEngine -  chr4:123857249        5.07e+07   21.6 m       25.5 s     26.3%        82.0 m    60.4 m 
INFO  16:08:08,739 TraversalEngine -  chr4:159136361        5.14e+07   22.1 m       25.8 s     26.9%        82.1 m    60.1 m 
INFO  16:08:39,042 TraversalEngine -  chr4:190981641        5.21e+07   22.6 m       26.0 s     27.4%        82.5 m    59.9 m 
INFO  16:09:09,130 TraversalEngine -   chr5:37183807        5.31e+07   23.1 m       26.1 s     28.0%        82.3 m    59.2 m 
INFO  16:09:39,133 TraversalEngine -   chr5:67589577        5.39e+07   23.6 m       26.2 s     28.6%        82.4 m    58.9 m 
INFO  16:10:09,165 TraversalEngine -   chr5:80762868        5.46e+07   24.1 m       26.5 s     29.1%        82.8 m    58.7 m 
INFO  16:10:39,166 TraversalEngine -  chr5:118835178        5.53e+07   24.6 m       26.6 s     29.6%        83.0 m    58.4 m 
INFO  16:11:09,216 TraversalEngine -  chr5:140050925        5.65e+07   25.1 m       26.6 s     30.3%        82.8 m    57.8 m 
INFO  16:11:39,294 TraversalEngine -  chr5:151125893        5.76e+07   25.6 m       26.6 s     30.9%        82.7 m    57.1 m 
INFO  16:12:09,341 TraversalEngine -  chr5:179013366        5.88e+07   26.1 m       26.6 s     31.7%        82.4 m    56.3 m 
INFO  16:12:39,407 TraversalEngine -   chr6:25779329        5.98e+07   26.6 m       26.7 s     32.3%        82.3 m    55.7 m 
INFO  16:13:09,494 TraversalEngine -   chr6:31970082        6.17e+07   27.1 m       26.4 s     33.0%        82.1 m    55.0 m 
INFO  16:13:39,517 TraversalEngine -   chr6:43271871        6.43e+07   27.6 m       25.7 s     33.9%        81.4 m    53.8 m 
INFO  16:14:09,679 TraversalEngine -   chr6:62442650        6.54e+07   28.1 m       25.8 s     34.4%        81.6 m    53.5 m 
INFO  16:14:39,746 TraversalEngine -   chr6:91233448        6.63e+07   28.6 m       25.9 s     35.0%        81.6 m    53.0 m 
INFO  16:15:09,785 TraversalEngine -  chr6:123658853        6.72e+07   29.1 m       26.0 s     35.6%        81.6 m    52.5 m 
INFO  16:15:39,789 TraversalEngine -  chr6:147042690        6.79e+07   29.6 m       26.1 s     36.2%        81.7 m    52.1 m 
INFO  16:16:09,839 TraversalEngine -  chr6:167570907        6.88e+07   30.1 m       26.3 s     36.8%        81.8 m    51.7 m 
INFO  16:16:40,040 TraversalEngine -   chr7:20687564        7.00e+07   30.6 m       26.2 s     37.5%        81.6 m    51.0 m 
INFO  16:17:10,069 TraversalEngine -   chr7:44294228        7.09e+07   31.1 m       26.3 s     38.1%        81.6 m    50.5 m 
INFO  16:17:40,277 TraversalEngine -   chr7:74943797        7.19e+07   31.6 m       26.4 s     38.7%        81.6 m    50.0 m 
INFO  16:18:10,352 TraversalEngine -   chr7:93518466        7.26e+07   32.1 m       26.5 s     39.3%        81.8 m    49.7 m 
INFO  16:18:40,483 TraversalEngine -  chr7:100676544        7.40e+07   32.6 m       26.4 s     39.8%        81.9 m    49.3 m 
INFO  16:19:10,512 TraversalEngine -  chr7:116960804        7.49e+07   33.1 m       26.5 s     40.3%        82.1 m    49.0 m 
INFO  16:19:40,584 TraversalEngine -  chr7:140373233        7.60e+07   33.6 m       26.5 s     41.0%        82.0 m    48.4 m 
INFO  16:20:10,634 TraversalEngine -  chr7:154774881        7.74e+07   34.1 m       26.4 s     41.6%        81.9 m    47.8 m 
INFO  16:20:40,686 TraversalEngine -   chr8:15519796        7.80e+07   34.6 m       26.6 s     42.1%        82.2 m    47.6 m 
INFO  16:21:10,741 TraversalEngine -   chr8:38034692        7.91e+07   35.1 m       26.6 s     42.8%        82.1 m    47.0 m 
INFO  16:21:40,826 TraversalEngine -   chr8:70488386        8.00e+07   35.6 m       26.7 s     43.4%        82.1 m    46.5 m 
INFO  16:22:10,877 TraversalEngine -  chr8:103281349        8.07e+07   36.1 m       26.8 s     44.0%        82.1 m    46.0 m 
INFO  16:22:40,886 TraversalEngine -  chr8:134145808        8.15e+07   36.6 m       26.9 s     44.5%        82.2 m    45.6 m 
INFO  16:23:10,963 TraversalEngine -   chr9:18661968        8.35e+07   37.1 m       26.7 s     45.4%        81.7 m    44.5 m 
INFO  16:23:41,037 TraversalEngine -   chr9:37442427        8.49e+07   37.6 m       26.6 s     46.0%        81.7 m    44.1 m 
INFO  16:24:11,114 TraversalEngine -   chr9:70871874        8.52e+07   38.1 m       26.8 s     46.3%        82.3 m    44.2 m 
INFO  16:24:41,129 TraversalEngine -   chr9:95418779        8.59e+07   38.6 m       27.0 s     46.9%        82.4 m    43.8 m 
INFO  16:25:11,139 TraversalEngine -  chr9:114151910        8.68e+07   39.1 m       27.0 s     47.5%        82.3 m    43.2 m 
INFO  16:25:41,161 TraversalEngine -  chr9:131343216        8.83e+07   39.6 m       26.9 s     48.3%        82.0 m    42.4 m 
INFO  16:26:11,278 TraversalEngine -   chr10:5789958        9.13e+07   40.1 m       26.4 s     49.4%        81.2 m    41.1 m 
INFO  16:26:41,348 TraversalEngine -  chr10:29169105        9.22e+07   40.6 m       26.4 s     50.0%        81.1 m    40.5 m 
INFO  16:27:11,402 TraversalEngine -  chr10:50599255        9.28e+07   41.1 m       26.6 s     50.5%        81.4 m    40.2 m 
INFO  16:27:41,436 TraversalEngine -  chr10:73892870        9.38e+07   41.6 m       26.6 s     51.1%        81.4 m    39.8 m 
INFO  16:28:11,443 TraversalEngine -  chr10:95069838        9.49e+07   42.1 m       26.6 s     51.8%        81.4 m    39.2 m 
INFO  16:28:41,461 TraversalEngine - chr10:105947244        9.66e+07   42.6 m       26.5 s     52.5%        81.1 m    38.5 m 
INFO  16:29:11,528 TraversalEngine - chr10:127797216        9.76e+07   43.1 m       26.5 s     53.2%        81.1 m    38.0 m 
INFO  16:29:41,638 TraversalEngine -   chr11:5718554        9.99e+07   43.6 m       26.2 s     54.0%        80.8 m    37.1 m 
INFO  16:30:11,704 TraversalEngine -  chr11:18420934        1.01e+08   44.1 m       26.2 s     54.7%        80.7 m    36.6 m 
INFO  16:30:41,725 TraversalEngine -  chr11:48131654        1.02e+08   44.6 m       26.1 s     55.4%        80.6 m    35.9 m 
INFO  16:31:11,837 TraversalEngine -  chr11:59829988        1.03e+08   45.1 m       26.3 s     55.8%        80.9 m    35.8 m 
INFO  16:31:41,883 TraversalEngine -  chr11:67258295        1.06e+08   45.6 m       25.8 s     56.8%        80.3 m    34.7 m 
INFO  16:32:12,167 TraversalEngine -  chr11:89534773        1.07e+08   46.1 m       25.8 s     57.6%        80.1 m    33.9 m 
INFO  16:32:42,291 TraversalEngine - chr11:108382050        1.08e+08   46.6 m       25.9 s     58.1%        80.3 m    33.7 m 
INFO  16:33:12,561 TraversalEngine - chr11:124056341        1.10e+08   47.1 m       25.8 s     58.8%        80.2 m    33.0 m 
INFO  16:33:42,578 TraversalEngine -   chr12:7060801        1.11e+08   47.6 m       25.7 s     59.6%        80.0 m    32.4 m 
INFO  16:34:12,625 TraversalEngine -  chr12:21422680        1.12e+08   48.1 m       25.7 s     60.1%        80.1 m    32.0 m 
INFO  16:34:42,737 TraversalEngine -  chr12:46231482        1.13e+08   48.6 m       25.8 s     60.7%        80.2 m    31.5 m 
INFO  16:35:12,768 TraversalEngine -  chr12:54967139        1.15e+08   49.1 m       25.5 s     61.5%        79.9 m    30.8 m 
INFO  16:35:42,823 TraversalEngine -  chr12:68052355        1.17e+08   49.6 m       25.4 s     62.1%        79.9 m    30.2 m 
INFO  16:36:12,878 TraversalEngine -  chr12:97337512        1.18e+08   50.1 m       25.4 s     62.7%        79.9 m    29.8 m 
INFO  16:36:42,898 TraversalEngine - chr12:112669451        1.19e+08   50.6 m       25.4 s     63.4%        79.9 m    29.3 m 
INFO  16:37:12,953 TraversalEngine - chr12:131649715        1.21e+08   51.1 m       25.4 s     64.2%        79.7 m    28.5 m 
INFO  16:37:42,954 TraversalEngine -  chr13:34410256        1.22e+08   51.6 m       25.4 s     64.8%        79.6 m    28.0 m 
INFO  16:38:13,028 TraversalEngine -  chr13:57743317        1.23e+08   52.1 m       25.5 s     65.4%        79.7 m    27.6 m 
INFO  16:38:43,037 TraversalEngine - chr13:114164602        1.24e+08   52.6 m       25.5 s     66.1%        79.6 m    27.0 m 
INFO  16:39:13,074 TraversalEngine -  chr14:31070929        1.26e+08   53.1 m       25.4 s     66.8%        79.6 m    26.5 m 
INFO  16:39:43,174 TraversalEngine -  chr14:58471784        1.27e+08   53.6 m       25.4 s     67.4%        79.6 m    25.9 m 
INFO  16:40:13,260 TraversalEngine -  chr14:75276076        1.28e+08   54.1 m       25.4 s     68.1%        79.5 m    25.4 m 
INFO  16:40:43,295 TraversalEngine - chr14:101370029        1.29e+08   54.6 m       25.4 s     68.8%        79.4 m    24.7 m 
INFO  16:41:13,352 TraversalEngine -  chr15:31198095        1.30e+08   55.1 m       25.4 s     69.5%        79.4 m    24.2 m 
INFO  16:41:43,378 TraversalEngine -  chr15:43328716        1.32e+08   55.6 m       25.3 s     70.1%        79.3 m    23.7 m 
INFO  16:42:13,415 TraversalEngine -  chr15:52903468        1.33e+08   56.1 m       25.3 s     70.7%        79.4 m    23.3 m 
INFO  16:42:44,145 TraversalEngine -  chr15:69011163        1.34e+08   56.7 m       25.3 s     71.3%        79.4 m    22.8 m 
INFO  16:43:14,184 TraversalEngine -  chr15:84657398        1.35e+08   57.2 m       25.3 s     72.1%        79.3 m    22.2 m 
INFO  16:43:44,195 TraversalEngine -    chr16:789692        1.37e+08   57.7 m       25.2 s     72.8%        79.2 m    21.5 m 
INFO  16:44:14,225 TraversalEngine -  chr16:15931975        1.40e+08   58.2 m       24.9 s     73.8%        78.8 m    20.6 m 
INFO  16:44:44,456 TraversalEngine -  chr16:22530534        1.41e+08   58.7 m       25.0 s     74.2%        79.1 m    20.4 m 
INFO  16:45:14,472 TraversalEngine -  chr16:47292530        1.43e+08   59.2 m       24.9 s     75.0%        78.9 m    19.7 m 
INFO  16:45:44,571 TraversalEngine -  chr16:69143290        1.45e+08   59.7 m       24.7 s     75.9%        78.6 m    19.0 m 
INFO  16:46:14,592 TraversalEngine -  chr16:84228835        1.46e+08   60.2 m       24.7 s     76.5%        78.6 m    18.5 m 
INFO  16:46:44,605 TraversalEngine -   chr17:7160372        1.49e+08   60.7 m       24.5 s     77.5%        78.2 m    17.6 m 
INFO  16:47:14,708 TraversalEngine -  chr17:16635202        1.51e+08   61.2 m       24.4 s     78.3%        78.2 m    17.0 m 
INFO  16:47:44,740 TraversalEngine -  chr17:30202424        1.53e+08   61.7 m       24.3 s     79.0%        78.0 m    16.4 m 
INFO  16:48:14,838 TraversalEngine -  chr17:39086206        1.54e+08   62.2 m       24.2 s     79.7%        78.0 m    15.9 m 
INFO  16:48:45,028 TraversalEngine -  chr17:45198290        1.56e+08   62.7 m       24.1 s     80.4%        78.0 m    15.3 m 
INFO  16:49:15,072 TraversalEngine -  chr17:60683461        1.57e+08   63.2 m       24.1 s     81.1%        77.9 m    14.7 m 
INFO  16:49:45,126 TraversalEngine -  chr17:74570515        1.60e+08   63.7 m       23.9 s     82.0%        77.7 m    14.0 m 
INFO  16:50:15,153 TraversalEngine -  chr18:13741552        1.62e+08   64.2 m       23.8 s     82.9%        77.4 m    13.2 m 
INFO  16:50:45,254 TraversalEngine -  chr18:44549376        1.63e+08   64.7 m       23.9 s     83.5%        77.5 m    12.8 m 
INFO  16:51:15,260 TraversalEngine -   chr19:2189732        1.64e+08   65.2 m       23.8 s     84.4%        77.2 m    12.0 m 
INFO  16:51:45,325 TraversalEngine -   chr19:9868613        1.66e+08   65.7 m       23.7 s     85.4%        76.9 m    11.3 m 
INFO  16:52:15,331 TraversalEngine -  chr19:17394596        1.69e+08   66.2 m       23.5 s     86.4%        76.6 m    10.4 m 
INFO  16:52:45,420 TraversalEngine -  chr19:37240574        1.71e+08   66.7 m       23.4 s     87.4%        76.3 m     9.6 m 
INFO  16:53:15,438 TraversalEngine -  chr19:44099263        1.73e+08   67.2 m       23.3 s     88.2%        76.2 m     9.0 m 
INFO  16:53:45,501 TraversalEngine -  chr19:52497000        1.75e+08   67.7 m       23.2 s     89.4%        75.7 m     8.1 m 
INFO  16:54:15,518 TraversalEngine -  chr19:56466272        1.76e+08   68.2 m       23.2 s     89.9%        75.8 m     7.7 m 
INFO  16:54:45,558 TraversalEngine -   chr20:5922631        1.77e+08   68.7 m       23.2 s     90.6%        75.8 m     7.1 m 
INFO  16:55:15,579 TraversalEngine -  chr20:34090619        1.79e+08   69.2 m       23.2 s     91.4%        75.7 m     6.5 m 
INFO  16:55:45,612 TraversalEngine -  chr20:51871726        1.80e+08   69.7 m       23.2 s     92.2%        75.6 m     5.9 m 
INFO  16:56:15,615 TraversalEngine -  chr21:34030098        1.82e+08   70.2 m       23.1 s     93.0%        75.4 m     5.3 m 
INFO  16:56:45,671 TraversalEngine -  chr22:18081065        1.84e+08   70.7 m       23.1 s     93.9%        75.3 m     4.6 m 
INFO  16:57:15,726 TraversalEngine -  chr22:31859828        1.85e+08   71.2 m       23.0 s     94.8%        75.1 m     3.9 m 
INFO  16:57:45,732 TraversalEngine -  chr22:46804945        1.87e+08   71.7 m       23.0 s     95.7%        74.9 m     3.2 m 
INFO  16:58:15,748 TraversalEngine -   chrX:23018579        1.88e+08   72.2 m       23.0 s     96.5%        74.8 m     2.6 m 
INFO  16:58:45,753 TraversalEngine -   chrX:48979166        1.89e+08   72.7 m       23.0 s     97.1%        74.8 m     2.1 m 
INFO  16:59:15,801 TraversalEngine -   chrX:69424814        1.91e+08   73.2 m       23.0 s     97.6%        74.9 m   105.7 s 
INFO  16:59:45,908 TraversalEngine -  chrX:100615069        1.92e+08   73.7 m       23.1 s     98.2%        75.1 m    82.0 s 
INFO  17:00:16,016 TraversalEngine -  chrX:119206743        1.92e+08   74.2 m       23.2 s     98.7%        75.2 m    58.4 s 
INFO  17:00:46,123 TraversalEngine -  chrX:140995052        1.93e+08   74.7 m       23.2 s     99.2%        75.3 m    36.4 s 
INFO  17:01:16,288 DepthOfCoverageWalker - Printing summary info 
INFO  17:01:16,294 TraversalEngine - Total runtime 4511.74 secs, 75.20 min, 1.25 hours 
INFO  17:01:16,295 TraversalEngine - 3113436 reads were filtered out during traversal out of 392820507 total (0.79%) 
INFO  17:01:16,295 TraversalEngine -   -> 3113436 reads (0.79% of total) failing UnmappedReadFilter 

ls

-rw-r--r-- 1 lindenb users        8267 Mar  5 17:01 _jeter.coverage.sample_interval_statistics
-rw-r--r-- 1 lindenb users    12725188 Mar  5 17:01 _jeter.coverage.sample_interval_summary
-rw-r--r-- 1 lindenb users       11402 Mar  5 17:01 _jeter.coverage.sample_statistics
-rw-r--r-- 1 lindenb users         176 Mar  5 17:01 _jeter.coverage.sample_summary

Knime4bio

added two nodes for Knime4bio: read mpileup and smart numeric filtering: http://code.google.com/p/knime4bio/source/detail?r=220


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