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  • How do I find medium length somatic indels?

    I used IndelGenotyperV2 to find somatic indels. But the longest I find is 4bp. My reads are single 75bp exome reads. I am interested in indels around 20bp. Is that possible with my reads?

    I ran the mapping step with bwa-0.7.5 on default setting. Is that the cause? I heard that the -o and -e flags for bwa aln supposedly have something to do with indels. If so, how do I set it up to find indels around 20bp?

    Thanks a lot in advance!

  • #2
    try Pindel. there is no theoretical maximum deletion size. currently maximum insertion size for insertions is read length - 20.

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    • #3
      For single-end reads, try novoalign. You may also consider bwa-mem with (higher matching score):

      bwa mem -A2 -B3 -O5 -E1

      bwa-backtrack does not find a gap more than 4bp for single-end reads. Pindel would not work with single-end, as I remember (could be wrong).

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      • #4
        Strelka does a fantastic job of finding longer somatic indels: https://sites.google.com/site/strelk...variantcaller/

        For exome data, set the "isSkipDepthFilters" to 1 in order to skip depth filtration.

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        • #5
          I tried "bwa aln -e 50" and it seems to work. Is bwa_mem better than bwa for this? How so?

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          • #6
            Originally posted by ymc View Post
            I tried "bwa aln -e 50" and it seems to work. Is bwa_mem better than bwa for this? How so?
            Yes, that may work, but bwa-mem should be better, at least faster. Bwa and bwa-mem are completely different algorithms.

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