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MSMT_2021_DR_analyses.yaml
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variant_folder: /nfs/jbailey5/baileyweb/asimkin/msmt_projects/MSMT_561H_paper/variant
metadata_sheet: /nfs/jbailey5/baileyweb/asimkin/github_pipelines/MSMT_2021_DR_analyses/manuscript_metadata_attempted_samples.csv
heirarchy: 'Region:District:HF_name'
output_folder: experimental_output
#these are all the mutations that we want to analyze. Format is {mutation}_
#{metadata-column}:{column-filter}_{coverage_threshold}_{alternate_threshold}
#for example, if you wanted to know all of the samples from the 'region' column
#of the metadata (broken down by each region) that had at least a coverage of 3
#and an alternate count of 1 for the mutation dhfr-ts-Cys59Arg, you would enter
#dhfr-ts-Cys59Arg_Region:all_3_1 as the mutation name.
mutations:
- dhfr-ts-Cys59Arg_Region:all_3_1
- dhps-Ser436Phe_Region:all_3_1
- mdr1-Asn86Phe_Region:all_3_1
- dhps-Lys540Glu_Region:all_3_1
- dhfr-ts-Asn51Ile_Region:all_3_1
- dhps-Ile431Val_Region:all_3_1
- crt-Ile356Thr_Region:all_3_1
- crt-Ala220Ser_Region:all_3_1
- dhps-Ala613Ser_Region:all_3_1
- mdr1-Asp1246Tyr_Region:all_3_1
- k13-Pro574Leu_Region:all_3_1
- cytb-Val284Lys_Region:all_3_1
- mdr1-Ser1034Cys_Region:all_3_1
- k13-Cys469Tyr_Region:all_3_1
- pph-Val1157Leu_Region:all_3_1
- mcp-Asn252Asp_Region:all_3_1
- k13-Gly449Ala_Region:all_3_1
- fd-Asp193Tyr_Region:all_3_1
- k13-Cys580Tyr_Region:all_3_1
- k13-Asn537Asp_Region:all_3_1
- cytb-Tyr268Ser_Region:all_3_1
- crt-Gln271Glu_Region:all_3_1
- dhfr-ts-Ser108Thr_Region:all_3_1
- k13-Ala675Val_Region:all_3_1
- k13-Cys469Phe_Region:all_3_1
- k13-Pro527His_Region:all_3_1
- dhfr-ts-Ser108Asn_Region:all_3_1
- dhfr-ts-Ile164Leu_Region:all_3_1
- k13-Val568Gly_Region:all_3_1
- crt-His97Leu_Region:all_3_1
- crt-Met74Ile_Region:all_3_1
- dhps-Ala437Gly_Region:all_3_1
- crt-Ile218Phe_Region:all_3_1
- crt-Cys72Ser_Region:all_3_1
- crt-Cys101Phe_Region:all_3_1
- Sec14-Asn615Asp_Region:all_3_1
- k13-Arg622Ile_Region:all_3_1
- k13-Pro553Leu_Region:all_3_1
- PI4K-Ser915Gly_Region:all_3_1
- k13-Pro441Leu_Region:all_3_1
- k13-Asn458Tyr_Region:all_3_1
- k13-Ile543Thr_Region:all_3_1
- mdr1-Asn86Tyr_Region:all_3_1
- mdr1-Asn1042Asp_Region:all_3_1
- dhps-Ser436Ala_Region:all_3_1
- k13-Arg539Thr_Region:all_3_1
- dhfr-ts-Ala16Val_Region:all_3_1
- k13-Ala481Val_Region:all_3_1
- cytb-Tyr268Asn_Region:all_3_1
- crt-Asn75Glu_Region:all_3_1
- k13-Phe446Ile_Region:all_3_1
- k13-Asn537Ile_Region:all_3_1
- mdr2-Thr484Ile_Region:all_3_1
- crt-Thr93Ser_Region:all_3_1
- k13-Met476Ile_Region:all_3_1
- k13-Arg515Lys_Region:all_3_1
- cytb-Tyr268Cys_Region:all_3_1
- crt-Val73Leu_Region:all_3_1
- PF3D7-1451200-Asn71Asn_Region:all_3_1
- k13-Arg561His_Region:Kagera_3_1
- k13-Gly538Val_Region:all_3_1
- crt-Phe145Ile_Region:all_3_1
- crt-Lys76Thr_Region:all_3_1
- crt-Lys76Thr_Region:Kagera_3_1
- mdr1-Tyr184Phe_Region:all_3_1
- arps10-Val127Met_Region:all_3_1
- k13-Arg561His_Region:all_3_1
- dhps-Ala581Gly_Region:all_3_1
- k13-Tyr493His_Region:all_3_1
- crt-Met343Leu_Region:all_3_1
- pib7-Cys1484Phe_Region:all_3_1
- dhps-Ala613Thr_Region:all_3_1
- crt-Gly353Val_Region:all_3_1
- cytb-Met133Ile_Region:all_3_1
- crt-Arg371Ile_Region:all_3_1
- crt-His97Tyr_Region:all_3_1
- crt-Asn326Ser_Region:all_3_1
- Pfap2mu-Ser160Asn_Region:all_3_1
- kelch10-Pro623Thr_Region:all_3_1
- exo-Glu415Gly_Region:all_3_1
- fd-Asp193Tyr_Region:all_3_1
- mdr2-Thr484Ile_Region:all_3_1
- pib7-Cys1484Phe_Region:all_3_1
- pph-Val1157Leu_Region:all_3_1
- crt-Asn326Ser_Region:all_3_1
- crt-Ile356Thr_Region:all_3_1
prevalence_thresholds:
- PF3D7-1451200_10_3_3
- PI4K_10_3_3
- Pfap2mu_10_3_3
- Pfubp1_10_3_3
- Sec14_10_3_3
- arps10_10_3_3
- crt_10_3_3
- cytb_10_3_3
- dhfr-ts_10_3_3
- dhps_10_3_3
- exo_10_3_3
- fd_10_3_3
- k13_10_3_3
- kelch10_10_3_3
- mcp_10_3_3
- mdr1_10_3_3
- mdr2_10_3_3
- pib7_10_3_3
- pph_10_3_3
background_mutations:
- crt-Asn326Ser_Region:all_3_1
- crt-Ile356Thr_Region:all_3_1
- mdr2-Thr484Ile_Region:all_3_1
- pph-Val1157Leu_Region:all_3_1
- pib7-Cys1484Phe_Region:all_3_1
- fd-Asp193Tyr_Region:all_3_1
intersections:
'IRNL_Region:all_3_1':
- dhfr-ts-Asn51Ile_Region:all_3_1
- dhfr-ts-Cys59Arg_Region:all_3_1
- dhfr-ts-Ser108Asn_Region:all_3_1
- dhfr-ts-Ile164Leu_Region:all_3_1
'IRNGEG_Region:all_3_1':
- dhfr-ts-Asn51Ile_Region:all_3_1
- dhfr-ts-Cys59Arg_Region:all_3_1
- dhfr-ts-Ser108Asn_Region:all_3_1
- dhps-Ala437Gly_Region:all_3_1
- dhps-Lys540Glu_Region:all_3_1
- dhps-Ala581Gly_Region:all_3_1