I searched Biostars to find a best practice workflows for vcf calling but I didn't find what I need to know. I need to create bam/sam and vcf files from fastq files. I know that I should use bowtie/bwa, fastqc, samtools but in some tutorials I saw that they assign read groups but in some tutorials they didn't and many other different parameters which used.

I am afraid to do this job and get wrong results. I will appreciate if you tell me how can I find most recent methods or confirmed workflows to complete this job.