chromosome order for chromosomes with weird names

[efoss]

Build 37 of the human genome has chromosomes with names like "chr7_gl000195_random.fa" or "chrUn_gl000211.fa". Chromosome order required by GATK is chr1, chr2, chr3, ... chr22, chrX, chrY with chrM either before everything or after everything. Where should the strangely named chromosomes be for the correct GATK chromosome ordering?

Thanks.

Eric

[raonyguimaraes]

After the karyotypically sorted reference chromosomes ...

I would consider using the data from GATK for the analysis

ftp://ftp.broadinstitute.org/pub/seq...sembly19.fasta

And

ftp://ftp.ncbi.nlm.nih.gov/snp/organ.../00-All.vcf.gz