I am new in bioinformatics. Today I was studying variation calling fllowing "the biostars handbook", when I found a bug out of my knowledge. Here is my code which is almost the same with the book chapter 87 : Variant calling example.

# Get the reference sequence. 
efetch -db nuccore -format fasta -id $ACC | seqret -filter -sid $ACC > $REF

# Index reference for the aligner. 
bwa index $REF 

# Index the reference genome for IGV
samtools faidx $REF

# Get data from an Ebola sequencing run.
fastq-dump -X 100000 --split-files $SRR

# Shortcut to read names.
R1=${SRR}_1.fastq
R2=${SRR}_2.fastq

# Align and generate a BAM file. 
bwa mem $REF $R1 $R2 | samtools sort > $BAM

 # Index the BAM file. 
samtools index $BAM

# Determine the genotype likelihoods for each base. 
bcftools mpileup -Ov -f $REF $BAM > genotypes.vcf

 # Call the variants with bcftools. 
bcftools call --ploidy 1 -vm -Ov genotypes.vcf > variants1.vcf

When I view the resulting VCF file in IGV, I got "No variants found":

I can tell that my igv is good, that is I think it's the problem caused by other reasons. Good wishes for you!