DepthOfCoverage (without -L option) output

fulviodanfulviodan ItalyPosts: 3Member

Hi there!
I tried to analyse the depth of coverage of my exome data using GATK DepthOfCoverage

java -Xmx${heap}m \
-Djava.io.tmpdir=$processed_bam/tmp_folder_dept \
-jar $gatk \
-T DepthOfCoverage \
-omitBaseOutput \
-omitLocusTable \
-R $GRCh37_ref_WholeGenome \
-I $file \
-o $coverage/${samplename}.coverage.dept

I am not interested in particular genomic regions, so I haven't a target list file.
How were the intervals determined in "_interval_statistics" output file?
Where can I obtain an interval target list file including all exons in the human genome?
Thank you very much!

Fulvio

Best Answers

Answers

  • fulviodanfulviodan ItalyPosts: 3Member

    Hi Geraldine, thanks for your prompt reply!

    I think if I set -omitIntervals -omitBaseOutput -omitLocusTable options, I'll obtain no results, isn't it?

    I'm not interested in specific intervals, but I would obtain a coverage for all exons. Could it fuction using for the -L option an exon list in bed format downloaded from UCSC?

    Don't you know what are the intervals generated in that "_interval_statistics" output?
    Source_of_reads from_0_to_1) from_1_to_2) from_2_to_3) from_3_to_4) ...

    Thanks!

    Fulvio

  • fulviodanfulviodan ItalyPosts: 3Member

    Ah, ok! It does not matter, It was only a curiosity! However the generated intervals are

     from_0_to_1) ... from_500_to_inf
    

    so they don't correspond to chromosomes.

    Best regards!

    Fulvio

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,364Administrator, GATK Developer admin

    Hah, I guess I remembered wrong! We have a lot of different tools :)

    It must use individual loci then, which is obviously not useful.

    Good luck with your work!

    Geraldine Van der Auwera, PhD

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