any recommandation on variant caller for SOLiD data ?

[pandafengye]

I want to call rare variants (SNP and short indel) from pooled sample. I used SHRiMP2 to map color-space reads and got BAM file. The questions are:

1, What variant caller programs are recommanded for SOLiD data?

2, When general variant caller are used upon SOLiD data, do they utilize the information of CS, CQ tag in the BAM file? And is the information important for SOLiD variant calling?

3, I have tried to use Bambino but I can't tell whether the result is good or not. Does anyone tell me about Bambino?

[tonybolger]

I want to call rare variants (SNP and short indel) from pooled sample. I used SHRiMP2 to map color-space reads and got BAM file. The questions are:

1, What variant caller programs are recommanded for SOLiD data?

Since you're using SHRiMP2, i guess you've tried VARiD?