Is Dindel Still Preferred Over Gatk For Indel Calling?

Question

[Bioscientist]

Just to simplify the question: Is Dindel still preferred over GATK for indel calling right now in 2012?

Because I read Heng Li's post that he recommend Dindel saying Dindel's model is better, achieving better sensitivity and specificity. But that was 2 years ago, and seems GATK has been trying to implement Dindel model into GATK. I'm just curious if GATK has made it or not.

thx

[muenalan]

Just note: Dindel is illumina data specific and cannot handle solid/life data.

Answer 1

[Larry_Parnell]

Mills et al. built a custom variation discovery pipeline capable of detecting SNPs, INDELs, and transposon insertions from ABI trace data. That pipeline was used to identify 415,436 unique INDEL variants from DNA re-sequencing traces originally generated for SNP discovery projects. Later, these authors applied thier tool to DNA traces obtained from the NCBI trace archive to identify another 819.363 INDELs.