bad input error on the PrintRead step

y.songy.song Seoul, KoreaMember
edited January 2017 in Ask the GATK team

To detect the mutation on the bam file, I used GATK to calibrate the file currently. However, only one showed this kind of error when I used PrintRead mode. The version of program is 3.5

Input: java -Djava.io.tmpdir=./scratch -Xmx4g -jar -GenomeAnalysisTK.jar \
-R ucsc.hg19.fasta \
-T PrintReads \
-I C2_fixed.bam \
-BQSR C2_recal_data.grp \
-o C2_recalib.bam

Error occurred in this step was as below.
Bad input: The GATK report has an unknown/unsupported version in the header: chrM:66-526

Could you give me some comments about this problem? This is first time I got this kind of error.

Thanks in advance.

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Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @y.song
    Hi,

    Can you please post the header of C2_recal_data.grp? Also, I don't know if this will make a difference, but you can try outputting a .table instead of a .grp.

    -Sheila

  • y.songy.song Seoul, KoreaMember

    Sorry for late response. The header is as below.

    :GATKReport.v.1.1.5

    :GATKTable:2:17:%s:%s:;

    :GATKTable:Arguments:Recalibration argument collection values used in this run

  • SheilaSheila Broad InstituteMember, Broadie, Moderator
    edited January 2017

    @y.song
    Hi,

    Hmm. I don't see any chrM:66-526 in the header. Can you try with the latest version? Also, can you please post your BAM header and Fasta .dict file?

    Thanks,
    Sheila

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