Cheat Sheet for NGS data analysis

Question

[angsudas62]

Is there any complete code in Bash that shows how to use from fasQC, sra-toolkit, bowtie to Sam/Bam tools. A complete collection of basic pipe lines to analyse NGS data (from .sra file through .fastq, .sam, .bad, to .vcf file) that can helpfull to remember all basic syntax. I have searched in the whole internet. One such question is there in Biostar already but the links in the answers are broken and no more available. Please Provide it now if possible. If reality there is no such thing on the planet earth please show your interest in colaborate with me to make one!

[desouzareis.r]

Hi,

The GATK Best Practices Workflows was a good start point for me. All their code is on Github, however it is written in Workflow Description Language (WDL) but you can find the bash commands there. For example this is the workflow for germline snps and indels.