Exome SNP Calling

[ercfrtz]

Does anyone have any experience with SNP calling using GATK and exome sequencing data (illumina paired end)? We tried to run it through normally, like it was whole genome sequence and we did not get any SNPs called (the reads were aligned using bwa). Do we need to do anything with exome positions vs just the whole genome using an option like -L? Any help would be appreciated.

[Bukowski]

I get plenty of SNPs in an Illumina sequenced, bwa aligned exome with GATK, and I don't use intervals to restrict calling to the bait/target positions.

Care to share your workflow? Hard to diagnose otherwise.

[ercfrtz]

We did alignment using bwa run as default. We then used samtools to convert to bam and sort. Then we ran the file through picard AddOrReplaceReadGroups to fix the read groups so that GATK would like it. Then we ran the file through GATK using the UnifiedGenotyper using default options. Our GATK isn't the newest version. Is there an issue with older versions of GATK?

[Bukowski]

We did alignment using bwa run as default. We then used samtools to convert to bam and sort. Then we ran the file through picard AddOrReplaceReadGroups to fix the read groups so that GATK would like it. Then we ran the file through GATK using the UnifiedGenotyper using default options. Our GATK isn't the newest version. Is there an issue with older versions of GATK?

There are many issues with old versions of GATK, but having used most of them 'not calling genotypes' isn't one of them. Which version? Can you please post your UnifiedGenotyper command line?

To reiterate it is impossible to diagnose issues where you do not post what you're doing.

The first thing to do though is to update GATK, if you attempt to go for support on https://getsatisfaction.com/gsa it is the first thing they will tell you to do.