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  • Visualization of variants from varScan with IGV

    Hi all,

    I visualized the variant positions I got from varScan using IGV.
    I saw that they show different coverage from what I have detected using varScan (usually the IGV have higher coverage for both variant and reference).
    This was also the case when I only used filtering for variant base quality>=15 and the other filtering steps done by awk on the output files.

    Example:
    from varScan output:
    chr1 556810 T Y 4625 254 5.21% 2 2 30 30 0.98 1 1 2266 2359 3 251 C

    from IGV:

    chr1 556810:
    A: 169 (2%,0+,169-)
    C: 692 (8%, 5+, 687-)
    T: 7551 (90%, 4316+, 3225-)
    N: 0

    Does anyone know where I got wrong?

    Thanks in advance,
    Oz

  • #2
    Please do not submit the same post twice. Thank-you!

    Comment


    • #3
      I'm sorry,
      Oz

      Comment

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