How do I visualize variants from VCF file in IGV?

Question

[Fanta]

Following Chapter 107 of the Biostart Handboolk Variant Calling Example I have obtained a reference genome refs/AF086833.fa, I have aligned sequencing data againsta a reference, then compiled a file with variants variants1.vcf . How do I visualize the variants in the IGV (web application)?

I tryied by loading the reference refs/AF086833.fa from menu Genome -> Local file... and got the error Genome requires either a single JSON file or a FASTA file & index file.

This is all I have in my working directory

./AF086833.2.fasta
./align_against_ref.sh
./call_variants.sh
./download_seq_data.sh
./genotypes.vcf
./prepare.sh
./SRR1553500_1.fastq
./SRR1553500_2.fastq
./SRR1553500.bam
./SRR1553500.bam.bai
./variants1.vcf
./refs/AF086833.fa
./refs/AF086833.fa.amb
./refs/AF086833.fa.ann
./refs/AF086833.fa.bwt
./refs/AF086833.fa.fai
./refs/AF086833.fa.pac
./refs/AF086833.fa.sa

Answer 1

[Fanta]

The way to do it is to first go to Genome > Local File... and then select two files (at the same time): the FASTA file and its index (extension .fai).

Then go to Tracks > Local File... and then select the VCF file.