ERROR MESSAGE: Input files reads and reference have incompatible contigs

[aituka]

Hello,
I have to call variants from 454 data. Since I have no quality file, I use Bowtie2 for the alignement.

Then to call the variants, I tried with GATK/UnifiedGenotyper:

##### ERROR MESSAGE: Input files reads and reference have incompatible contigs: No overlapping contigs found.
##### ERROR reads contigs = [chr1, chr2, chr3, chr4, chr5, ...
##### ERROR reference contigs = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, ...

The problem comes from the fact that fasta index uses 'chr1,etc.' while the reference I used was the one provided by Ensembl which uses '1,2,etc.'. Then I used the fasta coming with Bowtie. But I got another problem with the dbsnp version:

##### ERROR MESSAGE: Input files dbsnp and reference have incompatible contigs: No overlapping contigs found.
##### ERROR dbsnp contigs = [1, 2, 3, 4,etc.
##### ERROR reference contigs = [chr1, chr2, chr3,etc.

The problem is that I can't find a version of dbsnp with 'chr'.
Question:
* is there a way to get dbsnp.vcf with 'chr'?
* is there a way to transform the .bam file such that chromosom are noted with '1,2,etc.'?

thank you,
bests,
tuka