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  • CASAVA v1.8 with indels

    My Settings :

    Biology : GAIIx, SureSelect capture, paired-end 2x76 with "in house" indexing

    BioInformatics : CASAVA v1.8 with ELANDv2, GenomeStudio

    My problem :

    One patient had a deletion (/ GCTGAG /) and an insertion (TTCATTCTGCAG) Del6ins12 in a "complicated" (See Illumina ) because there are a repetition before. At present, CASAVA v1.8 and therefore does not detect ELANDv2 (not reported!) a variation at this level .

    Do you know of a program (software, algorithms) that could detect such an anomaly?

    My sequence :

    agcttcttaggacagcacttcctgattttgttttcaacttctaatcctttgagtgtttttcattctgcagAT/GCTGAG/TTTGTGTGTGAACGGACACTGAAATATTTTCTAGGAATTGCGGGAGGAAAATGGGTAGTTAGCTATTTCTgtaag

    Also, is it possible to make the annotation (exon, intron, capture zones, etc.) in GenomeStudio?

    Thanks,

  • #2
    Try bwa for alignment, and either samtools or GATK for variant calling. I've found 7 base deletions fine with bwa+samtools.

    Comment


    • #3
      Originally posted by tonio100680 View Post
      My Settings :

      Biology : GAIIx, SureSelect capture, paired-end 2x76 with "in house" indexing

      BioInformatics : CASAVA v1.8 with ELANDv2, GenomeStudio

      My problem :

      One patient had a deletion (/ GCTGAG /) and an insertion (TTCATTCTGCAG) Del6ins12 in a "complicated" (See Illumina ) because there are a repetition before. At present, CASAVA v1.8 and therefore does not detect ELANDv2 (not reported!) a variation at this level .

      Do you know of a program (software, algorithms) that could detect such an anomaly?

      My sequence :

      agcttcttaggacagcacttcctgattttgttttcaacttctaatcctttgagtgtttttcattctgcagAT/GCTGAG/TTTGTGTGTGAACGGACACTGAAATATTTTCTAGGAATTGCGGGAGGAAAATGGGTAGTTAGCTATTTCTgtaag

      Also, is it possible to make the annotation (exon, intron, capture zones, etc.) in GenomeStudio?

      Thanks,
      CASAVA is getting better, but it's still not as good as BWA/Stampy/Novoalign + GATK

      see nature proceedings paper (still a work in progress and not peer reviewed!):

      Comment


      • #4
        Right now Dindel is probably your best bet when it comes to indels.

        Comment

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