Adding read group and Platform information

[sbaheti]

Hi

I am using BWA for alignment of my *.fastq files to get *.sam as an output. I have observed that *.sam lacks the RG and PL header.

My Fastq looks like this
@R0174436_0092:1:2:853:5576#0/1
NACAACTTGAAGCAAAGGCAGGAAGCCTTGAAGCCGANNCAGAGAGGGGG
+R0174436_0092:1:2:853:5576#0/1
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB

and sam looks like this
(partial header)
@SQ SN:chr1 LN:247249719
@SQ SN:chr2 LN:242951149
@SQ SN:chr3 LN:199501827

R0174436_0092:1:2:853:5576#0 16 chr4 79804636 25 50M * 0 0 CCCCCTCTCTGNNTCGGCTTCAAGGCTTCCTGCCT
TTGCTTCAAGTTGTN BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB XT:A:U NM:i:3 X0:i:1 X1:i:0 XM:i:3 XO:i:0 XG:i:0 MD:Z:1
1C0T36C0

the BWA script i used

bwa aln -l 32 -t 4 genome sequence1 > aln_1.sai
bwa aln -l 32 -t 4 genome sequence2 > aln_2.sai
bwa sampe genome aln_1.sai aln_2.sai sequence1 sequence2 > out.sam

Do i need to add another index file or do i have some parameter to introduce to add RG and PL header to my sam file.

Thanks

Saurabh

[Brugger]

Please see http://seqanswers.com/forums/showthr...5327#post25327 for multiple solutions

[sbaheti]

Thanks Brugger !!, i will definitely try this..