Detecting Structural variants in sequencing data
Hello!
I am trying to find new tools for accurately calling structural variants in ~1000 samples sequencing data. LumpySV seems to perform better and could be the tool of choice but it requires BWA aligned BAM files only. Are there any other tools for calling structural variants with non BWA aligned BAM files.
Thanks!
1 answer
Try classical manta (https://github.com/Illumina/manta), gridss (https://github.com/PapenfussLab/GRIDSS).
Additionally, some SV callers based on deep learning are recently developed. You can try.
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you can try this . http://gmt.genome.wustl.edu/packages/pindel/ http://www.sanger.ac.uk/science/tools/pindel there are many other tools available you may need to spend some time on trying to find one.
is it PINDEL or DINDEL? Both are for indel detection. For structural variation detection, here is the laundry list: https://omictools.com/structural-variant-detection-category
What type of SVs you are interested in? Copy number variation or rearrangements or both? Germline or somatic? If you have non BWA aligned BAM files you can realign data with BAM and use LumpySV if you are sure in its performance for your data.
There are plenty of SV callers available which use sequencing data. You need to be specific about your SV types, Somatic or Germline. You can always realign your fastq reads using a different aligner. Breakdancer, Lumpy, Delly, SVdetect, Pindel are some of popular SV callers.
Best.