Trace_data

# TRACE Data Resources ## Git Repos trace: This repo contains pip installable versions of TRACE algorithm https://github.com/YulinZhang9806/trace.git trace_paper: This repo contains analysis pipelines applied in the paper https://github.com/YulinZhang9806/trace_paper.git ### `tables` These consist of post-processed tables of archaic tract calls from the manuscript across all tested populations. The *t_{number}* in the filenames indicates the value of `t` used when running `trace-extract` to assign the focal branch timescale. `trace_t31500_den.csv` recorded inference results for super-archaic segments within Denisovan segments in Oceanians. Columns:- chromosome, start, end, mean_posterior, length(bp), length(cM): see outputs from trace-summary (git repo "trace")- hmmix_start, hmmix_end, hmmix_overlap_length(bp), mean_pp, hmmix_assign: The start, end positions, overlapping length, mean posterior probability and archaic ancestry assignment for segments from hmmix results of the same haplotype that overlaps the current TRACE output archaic segment- ibdmix_start, ibdmix_end, ibdmix_overlap_length(bp), ibdmix_max_length(bp), ibdmix_assign: The start, end positions, overlapping lengths, maximum length and archaic ancestry assignments for segments from IBDmix results of the same individual that overlaps the current TRACE output archaic segment- dsnps: derived mutations (all NA in these tables to reduce file sizes)- dsnps_marks: marks (ND00, ND01, ND10, ND11, other) for derived mutations- DAF_YRI: derived allele frequency for mutations in YRI samples included in the ARG- t1s: lower-end times of introgression branches in this segment- t2s: upper-end times of introgression branches in this segment- mutages: mutation ages for derived mutations- branch_mark: marks for derived mutations showing if they are mapped (on, above, below) the introgression branch- nderived, nderived_strict: number of derived alleles (that are in 1000 Genomes strict mask)- ND00, ND10, ND01, ND11, ND00_strict, ND10_strict, ND01_strict, ND11_strict: number of (ND00, ND01, ND10, ND11) mutations on the segment (that are in 1000 Genomes strict mask)- nd00_b, nd10_b, nd01_b, nd11_b, tot_b, yri_b: number of (ND00, ND01, ND10, ND11, total, shared with YRI) mutations mapped on the introgression branch- nd00_prop, nd10_prop, nd01_prop, nYRI: P_ND00, P_ND10, P_ND01 and P_nYRI values (see Supplementary Section S4.2 for definitions)- assign_label: archaic label assigned to the segment (NEA, DEN, Ghost; for trace_t31500_den.csv, NONE -- Denisovan, SUPER -- super-archaic)- samplename: sample name shown on the VCF file header- ID: haplotype sample ID (tree node ID) used in the ARG ## Contact For any questions contact the corresponding authors of the TRACE paper: - Yulin Zhang ([e-mail])- Arjun Biddanda ([e-mail])- Priya Moorjani ([e-mail])