Mismatch header after generating reference using GATK [FastaAlternateReferenceMaker]
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3.6 years ago


I try to use the command "FastaAlternateReferenceMaker" to build a new genome reference from FASTA+VCF. The commands that I used were:

samtools faidx Genome.fasta

java -jar /Users/picard/build/libs/picard.jar  CreateSequenceDictionary R=Genome.fasta O=Genome.dict

java -jar /Users/GenomeAnalysisTK-3.8/GenomeAnalysisTK.jar -T FastaAlternateReferenceMaker -R Genome.fasta -o Genome_new.fasta -V input.vcf

I already generated the reference genome using my WGS data as a template. However, the FASTA file that I got is somehow not matching to the database on PlasmoDB (the master reference). So, I cannot use the generated reference for further analysis. Do you have any suggestions or comments for this matter? I want to change the Chr name on my generated reference genome (Name as 1, 2, 3....) to the same as the PlasmoDB reference (Name as AABL......). The explanation is shown in the photo >> https://photos.app.goo.gl/yeBJn7S9QQE241AW7

Thank you very much


gatk FastaAlternateReferenceMaker fasta • 722 views

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