How are the variants called by samtools?

Question

[lakhujanivijay]

Sorry if this question sounds ridiculous but I am very much puzzled as how variants are called by samtools? I mean what is the correct path?

samtools mpileup created the mpileup file or vcf file which have the variants? What does BAQ does; I suppose it is bundled with samtools, is that correct?

Also, what does bcf tools call function does. I am totally confused at this point; please help

[Max Ivon]

Did you mean this?

samtools mpileup -d $coverage_max -L $coverage_max -E -uf reference.fasta input.bam -P ILLUMINA -Q 30 | bcftools view -bvgc - > calls.bcf
bcftools view calls.bcf | vcfutils varFilter -d 30 -a 10 -1 0.001 -2 0.001 -3 0 -4 0.0001 - > calls.vcf

[lakhujanivijay]

Yes, can you explain it a little bit like what parameter and what tool is doing what?