The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Powered by Vanilla. Made with Bootstrap.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.
Register now for the upcoming GATK Best Practices workshop, Feb 20-22 in Leuven, Belgium. Open to all comers! More info and signup at http://bit.ly/2i4mGxz

Realigning sample-merged bam files?

jschoenejschoene Roslin InstituteMember Posts: 1

Following GATK's best practices, I have individually realigned/recalibrated my sample-lane bams and merged them by sample:

sample1_lane1.dedup.realn.recal.bam -->
sample1_lane2.dedup.realn.recal.bam --> sample1.merged.bam
sample2_lane1.dedup.realn.recal.bam -->
sample2_lane2.dedup.realn.recal.bam --> sample2.merged.bam
...

I am ready to dedup and realign my sample merged bams, however I am uncertain on the best approach. Is the consensus to convert back to fastq via Picard (MarkDuplicates, SortSam, and SamToFastq) and then run bwa mem? Or is it more expedient/accurate to realign the sample-merged bam using bwa aln followed by bwa sampe?

Best Answer

Answers

Sign In or Register to comment.