missing header information in bam cause GATK unifiedgenotyper fail

[foxyg]

Hi, I am this mitochondria sequence data, aligned using only chrM reference using BWA, and aligned against HG19 using bwa.

The bam file header looks like
@SQ SN:chrM LN:16569

When I run gatk unifiedgenotyper, got this error message:
##### ERROR MESSAGE: SAM/BAM file SAMFileReader{/home3/guoy1/CaiMitochondria/analysis_chrM/SNPcall/../out.bam} is malformed: Read HWUSI-EAS614_0001:5:1:1051:19990#0 is missing the read group, which is required by the GATK

But when I use the the bam file from HG19
The header looks like
@SQ SN:chr1 LN:249250621
@SQ SN:chr2 LN:243199373
@SQ SN:chr3 LN:198022430
@SQ SN:chr4 LN:191154276
@SQ SN:chr5 LN:180915260
@SQ SN:chr6 LN:171115067
@SQ SN:chr7 LN:159138663
@SQ SN:chr8 LN:146364022
@SQ SN:chr9 LN:141213431
@SQ SN:chr10 LN:135534747
@SQ SN:chr11 LN:135006516
@SQ SN:chr12 LN:133851895
@SQ SN:chr13 LN:115169878
@SQ SN:chr14 LN:107349540
@SQ SN:chr15 LN:102531392
@SQ SN:chr16 LN:90354753
@SQ SN:chr17 LN:81195210
@SQ SN:chr18 LN:78077248
@SQ SN:chr19 LN:59128983
@SQ SN:chr20 LN:63025520
@SQ SN:chr21 LN:48129895
@SQ SN:chr22 LN:51304566
@SQ SN:chrX LN:155270560
@SQ SN:chrY LN:59373566
@SQ SN:chrM LN:16571

And no error for unifiedgenotyper. Both bam files don't have read group information in the headers, why would unifiedgenotyper complain about the chrM only one?

Anyone know anything please let me know.

Thanks

[lshen]

Is this related to this: "BWA patch to generate read group"

http://www.broadinstitute.org/gsa/wiki/index.php/BWA_patch_to_generate_read_group

[Michael.James.Clark]

My advice is to use the pre-produced genomes in the gatk_resources.tgz file you can obtain for their site. The program is too finicky if you try using something else in my experience. Also, you do need RG flags for it to work properly regardless. The link Ishen contributed explains how to add them downstream if you didn't add them when you did alignment. Good luck!

[SWP]

Is this related to this: "BWA patch to generate read group"

http://www.broadinstitute.org/gsa/wi...ate_read_group

Hello-

I've never used patch before. It told me 9 of 9 hunks (and then in subsequent attempts 7 of 7 hunks) failed. When I tried recompiling I got the following errors:

make[1]: Entering directory `/home/arup/software/bwa-0.5.8c'
make[1]: Nothing to be done for `lib'.
make[1]: Leaving directory `/home/arup/software/bwa-0.5.8c'
make[1]: Entering directory `/home/arup/software/bwa-0.5.8c/bwt_gen'
make[1]: Nothing to be done for `lib'.
make[1]: Leaving directory `/home/arup/software/bwa-0.5.8c/bwt_gen'
gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD bntseq.c -o bntseq.o
In file included from bntseq.c:32:
bntseq.h:87: error: conflicting types for ‘read_group_t’
bntseq.h:74: error: previous declaration of ‘read_group_t’ was here
bntseq.h:100: error: conflicting types for ‘read_group_t’
bntseq.h:87: error: previous declaration of ‘read_group_t’ was here
make: *** [bntseq.o] Error 1

Any suggestions?