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  • Filter for indels

    Dear all,

    I am looking at sequence data from a fungal microorganism strain mapped to an assembled reference genome sequence:
    Number of reads: 5.5 Mill Paired End
    Platform : Illumina HiSeq 2000
    Length read : 126 bp

    I want to retrieve the number of insertions / deletions between different strains and I applied BCFtools to list indels found with reasonable coverage in CDS regions. However, the identified indels are too many and not convincing as they include repetitions. (e.g. GCAACAGCAGCAACAGCAACAGCAGCAACA/GCA)

    Please also look at the attached IGV

    Do you know a way to filter meaningful indels? Which criteria would you apply?

    Best ; Tom
    Attached Files
    Last edited by mitchum20; 03-22-2018, 09:53 AM.

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