How to analyse the result of GATK by using the VarScan

[qingmei]

Dear all,
I have one sample genome sequence data which mapped into the reference genome, and I have called the SNP with GATK. However, its seems the GATK can only calling the SNP between sample and reference, but I want to calling the SNP among sample. And I try to analyse the result of GATK by using the VarScan, but its failure! Is there any softwares can do this job?
Thanks!

[dkoboldt]

Dear qingmei,

You can perform multi-sample SNP calling with a few different tools including SAMtools mpileup.

You can also analyze raw mpileup from multiple samples with VarScan as follows:

samtools mpileup -f reference.fa -q 1 sample1.bam sample2.bam sample3.bam >out.mpileup
java -jar VarScan.jar mpileup2snp out.mpileup >out.mpileup.snp

Sincerely,

Dan Koboldt

[qingmei]

Dear Dan,
Thank you very much for your help. The samtools can do the job, but I want to use the GATK soft which have the function of Base Quality Recalibration and Variant Recalibration for SNP calling. So, I want to know whether have methods to call the SNP among sample by using the GATK soft.
Thanks!