<jupyter_start><jupyter_text>Prioritizing Variants In Patient Genome Data<NAME>, CCBB, UCSD (<EMAIL>) Table of Contents* [Background](background)* [Decision Tree Development](decision-tree-development)    * [Version One](version-one)    * [Version Two](version-two)    * [Version Three](version-three)    * [Version Four](version-four)* [Next Steps](next-steps)  BackgroundI have been asked to help develop an in-house pipeline for DNA variant ranking.  The request was:> Simply put, we need to develop a consistent ranking strategy for DNA variants - perhaps one that mirrors the protocol at [ http://www.semel.ucla.edu/research/variant-filtering-ranking-pipeline ]. For the most part, Guorong has the pipeline built already for generating fully annotated variant tables ... [snip /] ... It’s a matter of coming up with the filtering rules on the columns of data. I read the link, which describes a four-tier filtering pipeline in which tier 1 is disruptive variants in coding exons (stop-gain, splice-site, short indels), tier 2 is damaging coding variants (predicted mis-sense), and tier 3 and 4 are variants conserved or accelerated in multiple lineages or just one lineage, respectively.  I've been asked to produce a decision tree, akin to this one shown in figure 10.20 of Exploring Personal Genomics (2013) by <NAME> and <NAME>:  ![](images/exploring_personal_genomics_by_dudley_fig_10-20.png) Information for making the scoring decisions is already being produced by our existing pipeline using the following call to annotate the .vcf variant file using ANNOVAR (see http://annovar.openbioinformatics.org/en/latest/ ):<jupyter_code>perl table_annovar.pl /mnt/data/workspace/data/normal_blood_wgs_hli_B1000000012_S1.final.vqsr.vcf.avinput humandb/ -buildver hg19 -out /mnt/data/workspace/data/normal_blood_wgs_hli_B1000000012_S1.vqsr_annotated -remove -protocol knownGene,tfbsConsSites,cytoBand,targetScanS,genomicSuperDups,gwasCatalog,esp6500siv2_all,1000g2014oct_all,snp138,ljb26_all,cg46,cg69,popfreq_all_20150413,clinvar_20150330,cosmic70,nci60 -operation g,r,r,r,r,r,f,f,f,f,f,f,f,f,f,f -nastring .<jupyter_output><empty_output>
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