GATK and ExomeCNV

[PandoraMid]

Hi, I'm trying to use ExomeCNV to detect the CNV on 2 chromosomes (13 and 17 for BRCA1 and BRCA2).

I use the manual on https://secure.genome.ucla.edu/index...CNV_User_Guide and for first part (the GATK part) I use the code on the instruction with the only variant on reference genome (I use hg19.fasta, is it correct?).

My output is

INFO  13:19:22,999 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  13:19:23,000 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.5-0-g36282e4, Compiled 2015/11/25 04:03:56 
INFO  13:19:23,001 HelpFormatter - Copyright (c) 2010 The Broad Institute 
INFO  13:19:23,001 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk 
INFO  13:19:23,003 HelpFormatter - Program Args: -T DepthOfCoverage -omitBaseOutput -omitLocusTable -R ../../../reference_genome/hg19.fasta -I ../OG040.bam -L ../../../reference_genome/exome.interval_list -o output_controllo.coverage 
INFO  13:19:23,005 HelpFormatter - Executing as martina@martina-X750JB on Linux 4.4.0-22-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14. 
INFO  13:19:23,005 HelpFormatter - Date/Time: 2016/05/17 13:19:22 
INFO  13:19:23,005 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  13:19:23,006 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  13:19:23,295 GenomeAnalysisEngine - Strictness is SILENT 
INFO  13:19:23,348 GenomeAnalysisEngine - Downsampling Settings: No downsampling 
INFO  13:19:23,352 SAMDataSource$SAMReaders - Initializing SAMRecords in serial 
INFO  13:19:23,369 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02 
INFO  13:19:23,381 IntervalUtils - Processing 18624 bp from intervals 
INFO  13:19:23,423 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files 
INFO  13:19:23,442 GenomeAnalysisEngine - Done preparing for traversal 
INFO  13:19:23,442 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] 
INFO  13:19:23,442 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining 
INFO  13:19:23,442 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime 
INFO  13:19:23,443 DepthOfCoverage - Per-Locus Depth of Coverage output was omitted 
INFO  13:19:42,619 DepthOfCoverage - Printing summary info 
INFO  13:19:43,028 ProgressMeter -            done     45657.0    19.0 s       7.1 m       99.9%    19.0 s       0.0 s 
INFO  13:19:43,028 ProgressMeter - Total runtime 19.59 secs, 0.33 min, 0.01 hours 
INFO  13:19:43,030 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 482973 total reads (0.00%) 
INFO  13:19:43,030 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter 
INFO  13:19:43,030 MicroScheduler -   -> 0 reads (0.00% of total) failing DuplicateReadFilter 
INFO  13:19:43,031 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter 
INFO  13:19:43,031 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter 
INFO  13:19:43,031 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter 
INFO  13:19:43,031 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter 
INFO  13:19:44,231 GATKRunReport - Uploaded run statistics report to AWS S3

Is it correct?

Then i proceed with the second part but when I try to load output.coverage.sample_interval_summary I have an error, in particular:

"The line 1 doesn't have 15 elements".

Where am I wrong?

Thank you for the help