Best Practices To Perform Exome Analysis (Illumina) Via Gatk

Question

[win]

hi all, I am trying to conduct exome analysis on NGS exome data. the was sent from the Illumina platform as a sorted bam file.

while referring to some of the "best ways" to analyze exome data, and particularly using GATK it seems that i might have to convert the bam -> sai and then realign and then once again create a bam file.

is there any way to use GATK and just use the sorted bam file as it already aligned and sorted.

new to this analysis so might have missed something, any advice in this area will be very appreciated.

A

[Sean Davis]

BAM files can contain unaligned or aligned reads. The most common form is the latter and I am almost sure that is the type you have. You'll need to familiarize yourself with samtools in order to be sure, though.

Answer 1

[JC]

Follow the GATK best practices, they have some suggestions for exome data.

Answer 2

[win]

thanks, I read the info at this link and understand it. however, it's still unclear to me if the Illumina sorted BAM file that I have would have to be realigned or if it can be used just as it.

[Sean Davis]

Only you can answer that question. You'll need to know how the sorted bam file was produced and then decide whether you think that is "correct" for your application. It is probably fine to use as is but you'll need to have the details of any analyses that have already been done for publication.

[win]

It seems the file is correctly aligned. However, when i try to run the following command java -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R hg19.fa -o sorted.bam.list -I sorted.marked.bam

I get an error message that states sam file does not have any read groups defined in the header.

Any ideas how this can be fixed?

[Sean Davis]

The picard AddOrReplaceReadGroups will allow you to add read groups to an existing BAM file.