I need to extract fasta sequences for two genes. I used
java -jar /Users/nuketbilgen/programs/GenomeAnalysisTK-3.3-0/GenomeAnalysisTK.jar -T FastaAlternateReferenceMaker -R $REF -o YK20.fasta -L bTau7_2and6_subset.bed -V YK20_S24S12.raw.g.vcf
but it does not seem to work all of the output fasta files have the same sequence as the reference. Is it because of the raw vcf file?