Skip to content

input format issue on qbasepileup indel mode  #305

Open
@ChristinaXu2017

Description

@ChristinaXu2017

Describe the bug
There was a option to specify the snp position file format and output format.
--is <somatic_indel_file> Path to somatic indel file and
--ig <germline_file> Path to somatic indel file and
--pindel adjust insertion position to conform to pindel format and
--gatk adjust insertion position to conform to gatk format and
--strelka adjust insertion position to conform to strelka format (same as pindel)

here pindel is a deprecated tool, so i tried gatk or strelka vcf files as input, eg.
--is <strelka vcf> --strelka ... or --ig <gatk vcf> --gatk ... but get same exception: 23:06:04.863 [main] INFO org.qcmg.qbasepileup.indel.IndelBasePileupMT - org.qcmg.qbasepileup.QBasePileupException: Could not determine the type of the DCC header. Not sure of the QCMGFlag column at org.qcmg.qbasepileup.QBasePileupUtil.parseDCCHeader(QBasePileupUtil.java:140)

To Reproduce
'java -jar $jar --log $output.log -m indel --strelka --is $somaticIndel --it $input_bam --og $output -r $reference -in $input_bam'

Expected behavior
indel mode should be deprecated, it seems only support dcc1 format which was our QCMG internal file and deprecated now.

Desktop (please complete the following information):

  • OS: mac or linux
  • Version : adamajava version 98-0412007c

Additional context
Add any other context about the problem here.

Activity

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

      Development

      No branches or pull requests

        Participants

        @ChristinaXu2017

        Issue actions

          input format issue on qbasepileup indel mode · Issue #305 · AdamaJava/adamajava