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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 
--summaryCoverageThreshold 10 
--summaryCoverageThreshold 30 
--summaryCoverageThreshold 50 
--interval_merging OVERLAPPING_ONLY 

Thanks again!



  • 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!


    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


  • chartlchartl 7ccMember mod

    Hi MarcelaD-

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


  • MarcelaDMarcelaD Member

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



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