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  • Mutation Detection Using Illumina Single-end Data

    Hi list,
    what would be the expected maximum deletion/insertion lenght that could be detected using 75bp single-end illumina reads using BWA/Samtools? Is it possible to maximize the size of the INDEL detected by modifying any alignment parameter without increasing the false positives too much?

    Looking forward to your thoughts,

    Dave

  • #2
    Generally speaking, paired-end data will let you find longer indels with much greater sensitivity and specificity than single-end reads.

    But here's a thread that might be of help which involves changing the gap extension penalties:

    Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc


    You might also want to try a simulation to test your detection rate.

    Comment


    • #3
      See also this thread for an alternate approach.

      Comment


      • #4
        Also, this paper



        for yet another approach (see Figure 2a for comparison of this (assembly) method versus alignment methods (1000 Genomes) )

        Comment

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