VCF files from pooled amplicon sequencing of the praziquantel molecular target TRPM_PZQ in schistosome populations from Western Kenya

This archive contains two variant call format (VCF) files generated from amplicon sequencing using pools of Schistosoma mansoni miracidia: PZQ_lab_amp_fb.atom.vcf: This VCF contains variants from experimental pools made of different proportions of SmLE-PZQ-ES and SmLE-PZQ-ER miracidia which differ at a single nucleotide polymorphism (741987 T>C) within Sm.TRPMPZQ. These pools were made of 0, 0.1%, 1%, and 10% SmLE-PZQ-ER and were indexed using either combinatorial (CDI) or unique (UDI) dual indexes to test their sensitivity in accurately detecting allele frequencies. PZQ_KE_amp_fb.atom.vcf: This VCF contains variants from field miracidia pools from hotspot and non-hotspot villages in western Kenya (Kisumu region). For each village, we generated triplicate pools (A, B, C) as biological replicates and for each pool, we performed duplicated PCR (1, 2) of the different loci (technical replicates). We amplified exons encoding the S1-S6 and TRP box of the Sm.TRPMPZQ, which are the domains directly interacting with praziquantel. The sequencing data for the two types of experiment were processed similarly: primers were removed using cutadapt, reads were aligned against the reference genome (S. mansoni v7 reference genome, WBPS release 14), variants were called using Freebayes, and multi-allelic sites and complex variants were normalized, split and atomized using BCFtools. The overall goal of the project was to analyze samples from hotspot (persistent transmission despite rounds of praziquantel treatment) and non-hotspot villages to investigate whether the difference could be due to resistance mutations within the target of praziquantel, the TRP channel Sm.TRPMPZQ. More information is available in the associated publication and code.