Best practices and programs tu run a WGS genetic analysis

Question

[Antonio R. Franco]

I had my own whole genome sequenced through Illumina 2x150 paired reads. Coverage is around 32X

I would like to analyze this genome, and would like to ask you for some advice, best practices, recommended mapper, variant databases that I can use and anything that can help me out in this road

I am planning in using a regular mapper such as bowtie2 or BWA, generate the VCF files using bcftools, databases such as ClinVar and the like, etc

Answer 1

[Pierre Lindenbaum]

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

An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing

[Antonio R. Franco]

Seems nice, thank you

Answer 2

[amy__]

This paper is good: https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-020-00791-w and also https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2928-9

[Antonio R. Franco]

Thank you !!

Answer 3

[Antonio R. Franco]

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4544753/pdf/nihms697486.pdf