quick question about merging bam files

[cli]

Hi, all,

I have multiple individuals from different populations. I have done BWA mapping with -R "@RG\tID:samplename\tSM:samplename\tPL:ILLUMINA". Then I transform the sam files to bam files using picard:

for i in *.sam;
do java -Xmx4g -Djava.io.tmpdir=/tmp \
-jar ./SortSam.jar \
SO=coordinate \
INPUT=${i%.sam}.sam \
OUTPUT=${i%.sam}.bam \
VALIDATION_STRINGENCY=LENIENT \
CREATE_INDEX=true;
done

My question is when should I merge all bam files into one. Should I do it before "marking PCR duplicates", "local realignment around indels" and "quality score recalibration", or after these steps? Thanks for help!

[dpryan]

It'd be best to simply reference the GATK best practices. Regarding marking duplicates, you definitely want to do that before merging.