FastaAlternateReferenceMaker gives the input sequence back without applying changes from vcf
I have sequencing reads (mapped with tophat/bowtie2 to reference genome) and from those created vcf files using samtools.
Now I have tried to get the fasta nucleotide sequence of a certain gene, for which I ran the following command with GATK v3.5-0
java -jar GATK -T FastaAlternateReferenceMaker -R Documents/sequencing/Pfalciparum.genome.fasta -o Documents/sequencing/CSP/CSP_NF166_GATK.fa -L Pf3D7_03_v3:221323-222516 -V Documents/sequencing/NF166.vcf
The output file is identical to the reference sequence at this locus, but from visual inspection of the aligned reads (bam file in IGV) I know where changes are expected. Any hints on what I might be doing wrong will be much appreciated.