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
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
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