Call variants 1.0 Call variants for a reference sequence with assembly Uses SAMTools mpileup, bcftools and vcfutils snp Input sequence Input reference sequence Sequence Nucleic Input assembly Input assembly (sorted BAM) Text Output variations Output variations Text '*.snp' Max number of reads per input BAM At a position, read maximally the number of reads per input BAM. (mpileup)(-d) Integer Minimum mapping quality Minimum mapping quality for an alignment to be used. (mpileup)(-q) Integer Min sample fraction Skip loci where the fraction of samples covered by reads is below FLOAT. (bcf view)(-d) Float Min read depth Minimum read depth. (varFilter) (-d) Integer Max read depth Maximum read depth. (varFilter) (-D) Integer