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  • Convert from baf to bam files

    Hi everyone,

    I'm trying to convert my baf files to bam, because i want to use dindel.

    So i use bfast to convert from baf to sam and samtools from sam to bam, but it failed at the bfast step...

    If someone knows a better tools or can help me.

    here my command line:
    Code:
    bfast bafconvert -O 4 -f /path_to/hg37all.fa files.baf
    The error:
    Code:
    ************************************************************
    Reading in reference genome from /path_to/hg37all.fa.nt.brg.
    In total read 26 contigs for a total of 3080452622 bases
    ************************************************************
    ************************************************************
    In function "readInReadGroup": Fatal Error[OpenFileError]. Message: Could not open file for reading.
    The file stream error was:: Bad address
     ***** Exiting due to errors *****
    ************************************************************
    I hav the right on all files...

    Thanks guys.

  • #2
    I try with bfat 0.6.4 e, i got the folowing error:
    ************************************************************
    Reading in reference genome from /pathto/bfast_indexes/hs_ref_37.fa.nt.brg.
    In total read 64 contigs for a total of 3099369125 bases
    ************************************************************
    Input:s_4_local.baf
    Output:s_4_local.sam
    Currently on:
    0Erreur de segmentation

    Comment


    • #3
      the end product of the bfast run is a SAM file (check the manual, page 52). I think you are leaving the "postprocess" part of the program. I then just use samtools to then convert SAM file to a BAM file.

      samtools view -bhS bfast.sam bfast.bam

      Comment

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