The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Did you remember to?


1. Search using the upper-right search box, e.g. using the error message.
2. Try the latest version of tools.
3. Include tool and Java versions.
4. Tell us whether you are following GATK Best Practices.
5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
6. For tool errors, include the error stacktrace as well as the exact command.
7. For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
8. For weird results, include an illustrative example, e.g. attach IGV screenshots according to Article#5484.
9. For a seeming variant that is uncalled, include results of following Article#1235.

Did we ask for a bug report?


Then follow instructions in Article#1894.

Formatting tip!


Surround blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ``` ) each to make a code block.
Powered by Vanilla. Made with Bootstrap.
Picard 2.9.0 is now available. Download and read release notes here.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

Depth of Coverage - reported only first exon

MarcelaDMarcelaD Member Posts: 14
edited May 2013 in Ask the GATK team

Hi there,

this is my interval_list

chr1 762095 762275 LINC00115|NR_024321
chr1 762280 762414 LINC00115|NR_024321
chr1 762420 762565 LINC00115|NR_024321
chr1 777259 777349 LOC643837
chr1 777391 777481 LOC643837
chr1 777482 777642 LOC643837

chr1 783061 783151 LOC643837
chr1 792270 792446 LOC643837
chr1 861266 861496 NM_152486|SAMD11
chr1 865582 865787 NM_152486|SAMD11
chr1 866331 866507 NM_152486|SAMD11

and this is the output from the sample_interval_summary

chr1:762095-762275 ...
chr1:762280-762414 ...
chr1:762420-762565 ...
chr1:777259-777349 ...
chr1:783061-783151 ...
chr1:792270-792446 ...
chr1:861266-861496 ...
chr1:865582-865787 ...
chr1:866331-866507 ...

why am I missing two exons?

this is my cmd:

java -Xmx32g -jar /local/apps/gatk/2.5-2-gf57256b/GenomeAnalysisTK.jar
-I sample.bam -R .../genome.fa -T DepthOfCoverage -o jtn
-geneList hg19.tsv -L exons.list
--omitDepthOutputAtEachBase --includeDeletions
--interval_merging OVERLAPPING_ONLY -l INFO

Thanks for your input!

/M

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,388 admin

    Hi Marcela,

    Please see the discussion here: http://gatkforums.broadinstitute.org/discussion/1831/depth-of-coverage-only-first-gene-summary-output

    I believe this is the same problem and can be solved the same way.

    Geraldine Van der Auwera, PhD

  • MarcelaDMarcelaD Member Posts: 14

    Thanks for your quick answer!

    The issue is that I do use a geneList file (hg19.tsv)

    -geneList

    666     LINC00115       chr1    +       762095  762565  762095  762565  3       762095,762280,762420,   762275,762414,762565,   0       |chr1:762095-762565|LINC00115|NR_024321|  cmpl    cmpl    0,0,0,
    666     LOC643837       chr1    +       777259  777642  777259  777642  3       777259,777391,777482,   777349,777481,777642,   0       |chr1:777259-777642|LOC643837|NR_015368|NR_047519|NR_047520|NR_047521|NR_047522|NR_047523|NR_047524|NR_047525|NR_047526|  cmpl    cmpl    0,0,0,
    666     LOC643837       chr1    +       783061  792446  783061  792446  2       783061,792270,  783151,792446,  0       |chr1:783061-792446|LOC643837|NR_015368|NR_047519|NR_047520|NR_047521|NR_047522|NR_047523|NR_047524|NR_047525|    cmpl    cmpl    0,0,
    666     NM_152486       chr1    +       861266  879593  861266  879593  13      861266,865582,866331,871064,874367,874612,876485,877519,877806,878173,878532,878657,879125,  861496,865787,866507,871262,874575,874816,876719,877733,878088,878465,878652,878777,879593,     0       |chr1:861266-879593|NM_152486|SAMD11|   cmpl    cmpl    0,0,0,0,0,0,0,0,0,0,0,0,0,

    So I do have a list of genes (hg19.tsv )and a list of exons or interval list (exons.list)

    And it only happens now and then, for instance for LINC00115 I do have the coverage at each exon

    Thanks!

  • CarneiroCarneiro Charlestown, MAMember Posts: 274 admin

    did this solve your problem? I'm afraid I didn't understand your answer.

  • MarcelaDMarcelaD Member Posts: 14

    Hi,

    sorry if I didn't explain my self, here I give it a try,

    This is my interval_list (-L) or exons:

    chr1 762095 762275 LINC00115|NR_024321 
    chr1 762280 762414 LINC00115|NR_024321 
    chr1 762420 762565 LINC00115|NR_024321 
    chr1 777259 777349 LOC643837 
    chr1 777391 777481 LOC643837 
    chr1 777482 777642 LOC643837 
    chr1 783061 783151 LOC643837 
    chr1 792270 792446 LOC643837 
    chr1 861266 861496 NM_152486|SAMD11 
    chr1 865582 865787 NM_152486|SAMD11 
    chr1 866331 866507 NM_152486|SAMD11

    Together with my -geneList (see above) I would expect 5 lines in the sample_interval_summary for LOC643837, but instead, I get 3, one for the first transcript (missing the last 2) and 2 for the second (correct output):

    chr1:762095-762275 ... 
    chr1:762280-762414 ... 
    chr1:762420-762565 ... 
    **chr1:777259-777349** ... 
    **chr1:783061-783151** ... 
    **chr1:792270-792446** ... 
    chr1:861266-861496 ... 
    chr1:865582-865787 ... 
    chr1:866331-866507 ..

    Why is that?

    Thanks again
    /M

Sign In or Register to comment.