ReadLengthDistribution

SystemSystem Posts: 226Administrator admin
edited July 2012 in Tool Bulletin

A new tool has been released!

Check out the documentation at ReadLengthDistribution.

Comments

  • jburattijburatti Posts: 4Member
    edited August 2013

    Hello,

    I'm wondering why the ReadLengthDistribution's output gives no readLength ?
    Here's an example:

    #:GATKReport.v1.1:1

    #:GATKTable:2:56:%s:%s:;

    #:GATKTable:ReadLengthDistribution:Table of read length distributions

    readLength LP6008435-DNA_D02

    null 817246042

    null 111823

    null 57440

    null 57384

    null 48292

    null 50990

    null 58112

    [...]

    Thanks

    Post edited by jburatti on
  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,187Administrator, GATK Dev admin

    Hi there,

    Can you tell me what version of GATK you are using, and what was your command line?

    Geraldine Van der Auwera, PhD

  • jburattijburatti Posts: 4Member

    Hi Geraldine,

    Here is my command line (I'm using GenomeAnalysisTK-2.6-5-gba531bd):

    GATK -T ReadLengthDistribution -R hg19.fa -I Sorted.Dedup.Realigned.bam -o Sorted.Dedup.Realigned.RLD.tbl

    Thanks

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,187Administrator, GATK Dev admin

    Hmm, this looks like it might be a bug. Could you please upload a test file so we can debug this locally? Instructions are in our FAQ on reporting a bug.

    Geraldine Van der Auwera, PhD

  • jreutherjreuther Posts: 3Member

    I am using the ReadLengthDistribution walker on the GenomeAnalysisTK-2.7-4-g6f46d11 version and also received the output of "NULL" as my read lengths. Is there a fix for this bug?

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,187Administrator, GATK Dev admin

    Not yet but it's on our to-do list to fix.

    Geraldine Van der Auwera, PhD

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,187Administrator, GATK Dev admin

    This is fixed in version 2.8. Sorry for the delay in posting the resolution notice.

    Geraldine Van der Auwera, PhD

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