[mira_talk] Re: miraconvert MAF into SAM - differing RG id ranges in SAM header and body
- From: "RIMBERT, Helene" <helene.rimbert@xxxxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Thu, 3 Jul 2014 07:42:31 +0000
Hi Bastien
I forgot to precise that the version of miraconvert I used here was from the
dev. binary you gave me on june 26th.
The miraconvert from v4.0.2 works fine!
So sorry for the misunderstanding.
Best regards,
Hélène
-----Message d'origine-----
De : RIMBERT, Helene
Envoyé : mardi 1 juillet 2014 14:18
À : 'mira_talk@xxxxxxxxxxxxx'
Objet : miraconvert MAF into SAM - differing RG id ranges in SAM header and body
Hi Bastien,
I have converted a 10 strains assembly MAF file into SAM using miraconvert and
i have noticed that the read group ID's are not the same between the header and
the body of the SAM file.
The RG ID's ranges from 1 to 10 in the header, while the RG:Z tag ranges from 2
to 11 thus leading to an error when using the BAM file with samtools mpileup:
[mpileup] 10 samples in 1 input files
<mpileup> Set max per-file depth to 800
[group_smpl] Read group 11 used in file assembly.depadded.bam but absent from
the header or an alignment missing read group.
Any help would be much appreciated !
Thank you in advance
Best regards,
Hélène
Hélène RIMBERT
Bioinformatics Engineer
Upstream Genomics
BIOGEMMA
Centre de Recherche
Route d'Ennezat
CS 90126
63720 CHAPPES
Tel: +33 (0)4-73-67-47-94
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