exonuc - christianparobek/cambodiaWGS GitHub Wiki

At the 2015 Trop Med we saw a presentation from Rick Fairhurst's group about an association between Art-R and the chr13 exonuclease Glu415Gly (E415G) marker. We looked at our CP groups and saw that all CP3 and CP4 were mutant, while CP1 was almost all wildtype and CP2 was mixed.

Now, for our resubmission at GBE, the reviewers want us to include this information. Here's how I'm doing it. Since our sample and call sets evolved from Fall 2015 until we submitted to GBE, I need to rerun the analysis using the most up-to-date VCF. Similar to the cambodiaWGS/resistance_genes analysis, I am looking for a specific locus so I will use all unfiltered data. In the cambodiaWGS/exonuclease folder, run this:

java -Xmx4g -jar ~/snpEff/snpEff.jar -v -o gatk Pf3D7v90 /proj/julianog/users/ChristianP/cambodiaWGS/pf/variants/our_goods_UG.vcf > our_goods_UG.anno.vcf
grep "E415G\|CHROM" our_goods_UG.anno.vcf > exo_results.txt