Read group

For example, to create a paired end same file with fully formatted read groups, you can run:

bwa sampe -i MARK -m DEPRISTO -l LIBRARY -p ILLUMINA -h Homo_sapiens_assembly18.fasta first.fastq.sai secondfastq.sai first.fastq second.fastq > pe.sam
This will result in a file that looks like:

@HD     VN:1.0  SO:unsorted
@SQ     SN:chrM LN:16571
@SQ     SN:chr1 LN:247249719
@SQ     SN:chr2 LN:242951149
[More @SQ lines removed for clarity]
@RG     ID:MARK SM:DEPRISTO     LB:LIBRARY      PL:ILLUMINA
61CC3AAXX100125:6:48:11631:21212        81      chrM    8       37      76M     chr17   21944837        0       GGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTATGCACGCGAT    99:<->=D>IF7.:7,H