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No heterozygous variants after converting vcf file to fasta
Now I'm struggling with a problem that when I converted a vcf file to fasta, I found there was not any heterozygous variants in the fasta file which was unexpected to see. Below was my flow of each step.
1. java -Xmx2g -jar GenomeAnalysisTK.jar -T SelectVariants -R Melc_scaffolds.fasta -V variant.vcf -o MD.vcf -sn MD
2. java -Xmx4g -jar GenomeAnalysisTK.jar -T FastaAlternateReferenceMaker -R Melc_scaffolds.fasta -V MD.vcf -o MD.fasta
These two stpes was according to this question https://gatkforums.broadinstitute.org/gatk/discussion/8035/vcf-to-fasta
what I don't understand is which command should I use "-trimAlternates"?
Above all, could anyone can tell me what I am doing wrong and what is the right way to have a correct fasta file?