CASAVA v1.8 with indels

[tonio100680]

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,

[swbarnes2]

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

[NGSfan]

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see nature proceedings paper (still a work in progress and not peer reviewed!):

http://precedings.nature.com/documents/6107/version/1

[gaffa]

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