SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
ExomeCNV: read.all.coverage problem mrfox Bioinformatics 3 01-27-2015 05:45 AM
issues on running ExomeCNV emilyjia2000 Bioinformatics 11 01-27-2015 05:16 AM
Error in ExomeCNV running croshong Bioinformatics 0 01-24-2014 07:10 AM
Problems running ExomeCNV lkadalayil Bioinformatics 2 07-23-2013 12:06 AM
Help needed for exomeCNV sht41 Bioinformatics 2 07-23-2013 12:04 AM

Reply
 
Thread Tools
Old 05-17-2016, 03:26 AM   #1
PandoraMid
Member
 
Location: Italy

Join Date: Nov 2015
Posts: 18
Default GATK and ExomeCNV

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

Code:
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 - [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
PandoraMid is offline   Reply With Quote
Reply

Tags
exome analsys, exomecnv, gatk

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 04:40 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO