Variations off GATK

[JohnK]

I have some Illumina data mapped via BowTie. Looking to call variations using the UnifiedGenotyper from GATK, but I keep getting this error:

Missing read group for read HWI-EAS392_0029_FC:4:95:12241:2946#ACTT

Any ideas?

[NGSfan]

I have some Illumina data mapped via BowTie. Looking to call variations using the UnifiedGenotyper from GATK, but I keep getting this error:

Missing read group for read HWI-EAS392_0029_FC:4:95:12241:2946#ACTT

Any ideas?

You need the add read groups to your SAM/BAM file. This was a pain in the butt in the beginning if you are not used to it - especially if you analyze only one sample at a time. I had to go back and redo all my analysis.The GATK have made it mandatory now.

Actually, it's a good idea to do anyway - helps you track your reads and helps with more complex downstream analysis. You need to look into adding it through the Bowtie command line (see the manual and help). Each program has a different way of doing it.

Basically it means adding a line to your SAM file, eg:

@RG ID:25291 SM:J00066 LB:LIB056 PL:illumina

The fields ID SM and LB are arbitary.. but PL: is sequencing platform specific and necessary.

[JohnK]

You need the add read groups to your SAM/BAM file. This was a pain in the butt in the beginning if you are not used to it - especially if you analyze only one sample at a time. I had to go back and redo all my analysis.The GATK have made it mandatory now.

Actually, it's a good idea to do anyway - helps you track your reads and helps with more complex downstream analysis. You need to look into adding it through the Bowtie command line (see the manual and help). Each program has a different way of doing it.

Basically it means adding a line to your SAM file, eg:

@RG ID:25291 SM:J00066 LB:LIB056 PL:illumina

The fields ID SM and LB are arbitary.. but PL: is sequencing platform specific and necessary.

Sweet! This sucks but thank you very much! Going to work on it now...