Is there a full one link for exome raw fastq to vcf pipleine in gatk?

Question

[Tania]

Hi Everyone

I am new to exome data variant calling. I usually start from a given vcf. I am looking for GATK Pipleine and it has many links, for this link, https://software.broadinstitute.org/gatk/best-practices/workflow?id=11165

and this full one but no code: https://software.broadinstitute.org/gatk/documentation/article.php?id=7870

Is there a link for the complete detailed pipleine with code snapshots and I can't find it?

Thanks

[GenoMax]

What about this one?

[Tania]

I added it above, its doing some test, assuming you have your bams, and doesn't show base recabiliaration code and various steps. I have the pipeline for RNAseq variant calling GATK, i starts from raw reads and give steps till the end, can't find similar one for exome data. Thanks,

Answer 1

[Pierre Lindenbaum]

everything under: https://github.com/gatk-workflows Examples use WDL , the format used by the cromwell workflow engine.

[Tania]

I was looking for something like this https://software.broadinstitute.org/gatk/documentation/article.php?id=3891 but for exome, I am still confused with the github, where is the code snapshots and description.