linux command line for analyzing WES data

Question

[Raheleh]

Hello there,

I have 76 WES data from tumor samples along with matched ones (paired-end, illumina) to find somatic and germline variations. Is there any article that provide the linux command line for analyzing WES data? Something like this article “https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5032908/” which provided the command line for the whole analysis of RNA-seq data analysis.

Any suggestions will be very appreciated!

[cpad0112]

I hope you know WES and RNA-seq data analysis are two different things. HISAT-STRINGTIE-BOWTIE workflow was mentioned in the manuscript and example cli script for HISAT2-STRINGTIE-Ballgown workflow (based on Griffith lab exercise on RNAseq) is here: https://digibio.blogspot.com/2017/10/rnaseq-data-analysis-tuxedo-new-protocol.html. For WES, i would recommend https://software.broadinstitute.org/gatk/best-practices/workflow?id=11145.

[Benn]

Have you tried GATK? https://software.broadinstitute.org/gatk/best-practices/