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problem with FastaAlternateReferenceMaker

Hi,

I'm trying to use FastaAlternateReferenceMaker to generate an alternate reference from VCFs files.
Unfortunately I get an error message:

ERROR MESSAGE: Input files variant and sequence have incompatible contigs. Please see http://gatkforums.broadinstitute.org/discussion/63/input-files-have-incompatible-contigsfor more information. Error details: The contig order in variant and sequenceis not the same; to fix this please see: (https://www.broadinstitute.org/gatk/guide/article?id=1328), which describes reordering contigs in BAM and VCF files..
ERROR variant contigs = [chr_21, chr_20, chr_19, chr_18, chr_17, chr_16, chr_15, chr_14, chr_13, chr_12, chr_11, chr_10, chr_9, chr_8, chr_7, chr_6, chr_5, chr_4, chr_3, chr_2, chr_1]
ERROR sequence contigs = [chr_1, chr_10, chr_11, chr_12, chr_13, chr_14, chr_15, chr_16, chr_17, chr_18, chr_19, chr_2, chr_20, chr_21, chr_3, chr_4, chr_5, chr_6, chr_7, chr_8, chr_9]

I don't understant because I've checked the order of the contigs in my reference sequence and it gives me this:

chr_21 dna:chromosome chromosome:MG2:21:1:409213:1
chr_20 dna:chromosome chromosome:MG2:20:1:472105:1
chr_19 dna:chromosome chromosome:MG2:19:1:549847:1
chr_18 dna:chromosome chromosome:MG2:18:1:573698:1
chr_17 dna:chromosome chromosome:MG2:17:1:584099:1
chr_16 dna:chromosome chromosome:MG2:16:1:607044:1
chr_15 dna:chromosome chromosome:MG2:15:1:639501:1
chr_14 dna:chromosome chromosome:MG2:14:1:773098:1
chr_13 dna:chromosome chromosome:MG2:13:1:1185774:1
chr_12 dna:chromosome chromosome:MG2:12:1:1462624:1
chr_11 dna:chromosome chromosome:MG2:11:1:1624292:1
chr_10 dna:chromosome chromosome:MG2:10:1:1682575:1
chr_9 dna:chromosome chromosome:MG2:9:1:2142475:1
chr_8 dna:chromosome chromosome:MG2:8:1:2443572:1
chr_7 dna:chromosome chromosome:MG2:7:1:2665280:1
chr_6 dna:chromosome chromosome:MG2:6:1:2674951:1
chr_5 dna:chromosome chromosome:MG2:5:1:2861803:1
chr_4 dna:chromosome chromosome:MG2:4:1:2880011:1
chr_3 dna:chromosome chromosome:MG2:3:1:3505381:1
chr_2 dna:chromosome chromosome:MG2:2:1:3860111:1
chr_1 dna:chromosome chromosome:MG2:1:1:6088797:1

(the same in the index and in the dict)

Which is not the same order as it is told in the error.

And I've reordered my VCF in the same order.

this is the command I use:
java -Xmx6000m -jar ~/Soft/GATK/GenomeAnalysisTK.jar -T FastaAlternateReferenceMaker -R genome.fa -o alt_fasta/test.fa -V VCF/sample.vcf

Could you tell me what could be the cause of this error?
Thanks in advance.

Guillaume

Answers

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