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FastaAlternateReferenceMaker Bug

skenoyskenoy chinaMember
edited November 2014 in Ask the GATK team

my script:

java -jar gatk-nightly-2014-09-15/GenomeAnalysisTK.jar -T FastaAlternateReferenceMaker -R Capra_hircus_for_rnaseq.fa -o bg.fa --variant bg.vcf

my chrs order of genome fasta(Capra_hircus_for_rnaseq.fa) is chr10 chr11 chr 12...
and chrs order of outfile(bg.fa) is chr1 chr2 chr3 chr4 ...

but it`s different bwteen chr10(genome) and chr10(outfile)

example:
genome chr10:

chr10

AAAATAGGTAGCAAAGGGAGTGCTGTCGAGTTGCCATAGGGGTCTGTAGCTTTCTCTTTAGGTGCCACAGGGCT...

outfile chr1:

chr1

AAAATAGGTAGCAAAGGGAGTGCTGTCGAGTTGCCATAGGGGTCTGTAGCTTTCTCTTTAGGTGCCACAGGGCT...

it might be wrong order between genome and outfile!!!

i dont find any options to fix it order on web.

Answers

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