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[TEST] Create a mini example for different SV types #57

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Irallia opened this issue Feb 11, 2021 · 0 comments · Fixed by #47 or #58
Closed
5 tasks

[TEST] Create a mini example for different SV types #57

Irallia opened this issue Feb 11, 2021 · 0 comments · Fixed by #47 or #58
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@Irallia
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Irallia commented Feb 11, 2021

  • Add a parameter, that we can specify a SV length, the default remains at 30bp.
  • Created a small example for different types of SVs: Deletion, Insertion, Duplication, Translocation, Duplication in the Referece
  • Create a VCF for the resulting junctions
  • Test the sam with samtools and look at it via IGV
  • Write a test case for the example file

A call should look something like this:

./bin/detect_breakends ~/Repos/iGenVar/test/data/mini_example.sam ~/.../mini_out.fasta > ~/.../mini_junctions.vcf -l 10
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