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  • Chromosomal notation and Segmentation fault

    Hi all,

    I have a bam file with chromosomal notation 1,2.... and i need it to be as chr1,chr2.....

    For this i have tried, samtools view -H sample.bam > header.sam

    Then edited the header.sam file with required chromosomal notation and tried samtools reheader header.sam sample.bam > out.bam

    when in tried to view out.bam using samtools it says "Segemntation fault".

    I also tried with PICARD, java -Xmx4g -jar ReplaceSamHeader.jar INPUT=sample.bam HEADER=header.sam OUTPUT=out.bam CREATE_INDEX=TRUE

    It reports the same error with samtools i.e. segmenation fault.

    Could anyone help me to fix this?

  • #2
    I got the same problem...

    Finally i gave up the reheader option. and use " cat header.sam sample.sam | samools view -S -b - >sample.bam" instead.
    Last edited by wangwl; 07-29-2013, 06:32 PM.

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