sirselim / diagnostics_exome_reporting

Pipeline to filter whole exome vcf files and generate a report document for clinical diagnostics.

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👋 Hi there! I'm Miles

I'm a bioinformatician / computational geneticist based in New Zealand. I am the Associate Director of the APAC Applications Project Support team at Oxford Nanopore Technologies. I also dabble at photography and guitar, with a side of coffee, beer and single malts in the mix.

I have written and maintiain several documents about GPU compute for Nanopore sequencing that people find helpful, feel free to check them out:

• GPU musings (with an eye on genomics)
• GPU price / performance comparisons for Nanopore basecalling
• Nanopore Guppy GPU basecalling on Windows using WSL2
• Nvidia Jetson Xavier Community Gist
• Nvidia Jetson Nanopore Sequencing - GitHub Repository

You can find out more about me and connect in different ways below:

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diagnostics_exome_reporting's Issues

Any 'local' interaction with GitHub repo requires ssh passphrase

Need to explore ways to allow either a single authentication per session or prevent the need for passphrase completely, i.e. rely on the ssh-keys and deploy set up on this repo.

A few places to start looking:

• http://rabexc.org/posts/using-ssh-agent
• http://sshmenu.sourceforge.net/articles/key-setup.html
• http://www.thegeekstuff.com/2008/11/3-steps-to-perform-ssh-login-without-password-using-ssh-keygen-ssh-copy-id
• http://www.tecmint.com/ssh-passwordless-login-using-ssh-keygen-in-5-easy-steps/

Replace grep gene lists with tabix options

There is a large amount of time being spent working through the grep steps for the larger Tier gene lists, this is not best practice and wasteful.

Using tabix is much faster and will result in better overall functionality.

• issue with grep using gene lists (files) and vcf.gz
  • look into using tabix (MUCH faster)
  • extract list of genes from a bed file (with position info), i.e. grep -w -f 'gene_list.txt' UCSC_gene_positions_hg19.bed > gene_regions_hg19.txt
  • use: tabix -R gene_regions.txt variant.vcf.gz