Variant calling from Trios Data

[d_t_nguyen]

Dear all,
We have a trios (father:30x, mother:30x, and son:30x), and want to do snp calling, short indel calling and structural variation calling.

We find triosCaller is good for SNP calling, however, it does not work for indels and structural variations.

Do you have any suggestions for indel calling and structural variation calling for trios data.
Thanks a lot indeed,
Nguyen

[m_two]

Breakdancer, SquareDancer, CREST, Pindel, Varscan, and GATK

http://tvap.genome.wustl.edu/

http://www.broadinstitute.org/gatk/download