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GATK and ExomeCNV

PandoraPandora ItalyMember

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.php/ExomeCNV_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 [email protected] 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 - | 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 :)

Best Answers


  • SheilaSheila Broad InstituteMember, Broadie admin


    Yes, your command looks fine and the output (no reads filtered is fine). However, did you mark duplicates? The reference you used must be fine as long as you aligned your reads to it. (I'm guessing it is also fine because you did not get an error :smiley:

    I suspect the issue you are having is with the next step, the R command.


  • SheilaSheila Broad InstituteMember, Broadie admin

    Hi again,

    You should look into using the GATK tools for CNV! Here is a start :smile:


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    I think @Sheila means http://gatkforums.broadinstitute.org/gatk/categories/gatk-4-alpha (ReCapSeg is the old, pre-GATK version of the CNV tools).

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