Detecting Structural variants in sequencing data

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7.5 years ago

Glen ▴ 30

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!

structural variants sequencing calling SVs • 3.3k views

ADD COMMENT • link updated 7.1 years ago by Biostar 20 • written 7.5 years ago by Glen ▴ 30

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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.

ADD REPLY • link 7.5 years ago by badribio ▴ 290

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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

ADD REPLY • link 7.4 years ago by cpad0112 21k

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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.

ADD REPLY • link 7.1 years ago by Max Ivon ▴ 140

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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.

ADD REPLY • link 7.1 years ago by Samarth Kulshrestha ▴ 300

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