This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!
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.