Hello,
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
Nattawat