I am looking for a specific ~20bp deletion in Illumina 2x150 data. Coverage is over 10,000 X. I have at least one sample where it is present. I was previously able to capture 30bp deletions with BWA, so 20bp should not be too big, but BWA is not catching it this time for whatever reason. I then tried Bowtie 2, which was able to detect it. I am following both with realignment using GATK.
Since the only two aligners I tried (BWA and Bowtie) gave very different results, now I am thinking others may give even more differing results. I could just start testing them and see what happens, but I thought I should consult here first. Is there an optimal aligner for deletions of that size?
Since the only two aligners I tried (BWA and Bowtie) gave very different results, now I am thinking others may give even more differing results. I could just start testing them and see what happens, but I thought I should consult here first. Is there an optimal aligner for deletions of that size?
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