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  • cambyses
    Junior Member
    • Nov 2013
    • 4
    #1

    BGI / Complete Genomics / File conversion cgatools

    Hello,

    I few weeks ago I received the results of my Exome sequencing project.

    Can someone help me with the conversion to SAM/BAM format.

    This is an example of the files i've got:

    mapping_GS81299-FS3-L08_001.tsv
    reads_GS81299-FS3-L08_001.tsv

    build37.crr

    How to convert with evidence2sam? Didn't work out for me.

    I have a second question

    in the VCF file qual = '.'
    However, in another file they give a QUAL value for each allele. Does it make sense to make the total of these values and divide them by 2 to put the result in an standard VCF file?

    Thank you in advance for answering. I'm new in this domain.
    Tags: complete genomics, raw data conversion
  • cambyses
    Junior Member
    • Nov 2013
    • 4
    #2
    How to put a value for each allele in the qual field in a VCF file? Does this make sense?

    Thank you for any help.

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