hey,

I am curious, because the GEM-2-SAM converter adds a basic header to the SAM file and this is also included in the BAM.

When I do a

samtools view -H NA20805-NA20805.4.M_120208.bam

I get

@HD    VN:1.3
@SQ    SN:chr1    LN:249250621
@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:chr2    LN:243199373
@SQ    SN:chr20    LN:63025520
@SQ    SN:chr21    LN:48129895
@SQ    SN:chr22    LN:51304566
@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:chrX    LN:155270560
@SQ    SN:chrY    LN:59373566
@RG    ID:0    PG:GEM    PL:ILLUMINA    SM:0
@PG    ID:GEM    PN:gem-2-sam    VN:1.306

so basic chromosome information is contained. Is there a problem with this part of the header or is there other information missing ?

best,
-Thasso

2012/6/18 Tuuli Lappalainen <Tuuli.Lappalainen@unige.ch>
Hello,

Jonas pointed out that the GEM bam files don't have header lines, which
may be a problem in some cases. I uploaded a reference index file
(/upload/geuvadis/wp4_rnaseq/main_project/external_data/reference/hg19_AXYM.fa.fai)
that can be used at least in samtools as additional information so that
header info is not required, or you can also use that to add headers to
your bams if you like.

best regards,
Tuuli

Tuuli Lappalainen, PhD
Department of Genetic Medicine and Development
University of Geneva Medical School
CMU / Rue Michel-Servet 1
1211 Geneva 4
Switzerland
Tel. +41-(0)22-3795550
tuuli.lappalainen@unige.ch


On 6/18/12 11:29 AM, Jonas Carlsson wrote:
> Hello!
>
> When I tried to run QC-analysis on the GEM-files many of the analysis
> modules failed because there is no header in the .bam-files. Is this a
> mistake or by choice?
>
> /Jonas
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