Is there a full one link for exome raw fastq to vcf pipleine in gatk?
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6.2 years ago
Tania ▴ 180

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

exome data variant calling • 1.4k views
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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,

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6.2 years ago

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

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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.

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