Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

Depth of Coverage - _gene_statistics

MarcelaDMarcelaD Member
edited May 2013 in Ask the GATK team

Hi there!
Just wondering how to get the _gene_statistics file, I do get the _gene_summary. Do I need to add a flag?

java -Xmx32g -jar GenomeAnalysisTK.jar 
-I OB.bam 
-R genome.fa 
-T DepthOfCoverage 
-o OB 
-geneList hg19.tsv 
-L hg19.list 
--omitDepthOutputAtEachBase 
--includeDeletions 
--summaryCoverageThreshold 10 
--summaryCoverageThreshold 30 
--summaryCoverageThreshold 50 
--interval_merging OVERLAPPING_ONLY 
-l INFO

Thanks again!

/M

Answers

  • CarneiroCarneiro Charlestown, MAMember admin
    edited May 2013

    It looks like your command line is correct (although I got confused there for a second). What are the output files of your run ? and did the GATK complete successfully?

    ps: Sorry I edited your post, I did it so I could read your command line more clearly.

  • MarcelaDMarcelaD Member

    Edit it as much as you like!

    OB.sample_cumulative_coverage_counts
    OB.sample_cumulative_coverage_proportions
    OB.sample_gene_summary
    OB.sample_interval_statistics
    OB.sample_interval_summary
    OB.sample_statistics
    OB.sample_summary
    

    and yes, it completed succesfully (or at least it seems so)

    INFO  16:28:43,370 ProgressMeter -   chrY:59340373        2.10e+08   27.0 m        7.0 s    100.0%        27.0 m     0.0 s
    INFO  16:28:58,591 DepthOfCoverage - Printing summary info
    INFO  16:28:58,598 DepthOfCoverage - Printing locus summary
    INFO  16:28:58,645 ProgressMeter -            done        2.10e+08   27.3 m        7.0 s    100.0%        27.3 m     0.0 s
    INFO  16:28:58,645 ProgressMeter - Total runtime 1637.19 secs, 27.29 min, 0.45 hours
    INFO  16:28:58,760 MicroScheduler - 6164390 reads were filtered out during traversal out of 197704633 total (3.12%)
    INFO  16:28:58,761 MicroScheduler -   -> 6100421 reads (3.09% of total) failing DuplicateReadFilter
    INFO  16:28:58,761 MicroScheduler -   -> 63969 reads (0.03% of total) failing UnmappedReadFilter
    INFO  16:29:00,804 GATKRunReport - Uploaded run statistics report to AWS S3
    

    /M

  • chartlchartl 7ccMember mod

    Hi MarcelaD-

    Would it be possible to post the interval list and gene list?

    Chris

  • MarcelaDMarcelaD Member

    Hi there... have you had time to look at this?

    Cheers!

    /M

Sign In or Register to comment.