I am trying to call SNP using the SAM Tools → mpileup in Galaxy.
Since the input in mpileupI is BAM format, I converted FASTQ file to BAM format using NGS: Mapping → Map with BWA.
Thereafter, I used this BAM file in mpileupI creating a compressed BCF file, which was converted to VCF using SAM Tools → bcftools call. However, when I immport the VCF to IGV it says that variants were not found.
I would like to know whats is going on since I would to see variants.
thanks in advance!