Best practice in vcf calling - From fastq to vcf ?

Question

[amir.jebelli]

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.

[harold.smith.tarheel]

Best practices are dependent upon your variant caller. In addition to GATK, other popular variant callers include Samtools/BCFtools (workflow here), FreeBayes (here), and VarScan 2 (here).

[amir.jebelli]

Thanks a lot.

Answer 1

[andrew.j.skelton73]

If you're looking to do variant calling on your data, then check out the GATK best practises

[amir.jebelli]

Thanks, I should check both ways and compare the results.