Convert WGS fastq files to VCF

Question

[nankos77]

What is, currently, the best pipeline to convert the two fastq files of an Illumina WGS to a VCF files?

I see there is the GATK pipeline, powered by Terra.bio, but I understand will start from BAM file...

Answer 1

[Pierre Lindenbaum]

Sarek : https://github.com/nf-core/sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing