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FastaAlternateReferenceMaker generate a reference fasta rather than my sample haplotype fasta
Hi, I am using the following command, wanting to generate haplotype fasta for 97 samples:
java -Xmx25g -jar $gatk -T FastaAlternateReferenceMaker -R $ref_genome -o new_output.fasta --variant $vcf
Here are what I did to my .vcf file:
1) I keep all the meta-information
2) I only select a specific region in my .vcf file (around SNP sites within 3Mb in the reference genome)
I attached a .zip file containing the first 120 lines of my .vcf file, I do not know how do deal with this error.
Looking forward to professional guidance, thank you!