# README for Gardiner_et_al_2017_Watkins_exome_capture_SNP_calls_VCF Data description: SNP calls against IWGSC Chinese Spring RefSeq v1.0 chromosome parts from exome capture data of 103 accessions of the Watkins landrace collection. Raw reads generated by and published in "Hidden variation in polyploid wheat drives local adaptation" by Gardiner et al, Gigascience, 2017 (doi: 10.1101/gr.233551.117). Read alignment and SNP calling performed by Jemima Brinton. Contact: Jemima Brinton (j.brinton@kew.org) or Cristobal Uauy (cristobal.uauy@jic.ac.uk) Software versions used: hisat-2.0.4 samtools-1.5 freebayes-1.0.0 bcftools-1.3.1 Methods: - Read alignment performed with hisat-2.0.4 (reference used: IWGSC Chinese Spring RefSeq v1.0 chromosome parts; conversion coordinates of parts to full chromosomes below) - Output converted to BAM using samtools view -Shu and sorted using samtools sort - PCR duplicates removed using samtools rmdup - BAM files from replicate sequencing runs merged using samtools merge - SNP calling performed using freebayes (default settings). NB: SNP calling performed as part of a set of ~250 samples, including wheat landraces and modern cultivars. Data presented here is the subset of Watkins samples from Gardiner et al 2017. - Output converted to bcf using bcftools view -O u - Relevant samples extracted and converted to .vcf.gz using bcftools bcftools view -Oz -S NB: files provided are raw SNP calling output and have not been filtered for any quality measures (e.g. MAF, read depth, location etc). Sample names: Watkins accession ID followed by sample rep ID. e.g 1190166_1 = watkins accession 1190166, single sequencing rep; 1190181_1_2 = watkins accession 1190181, sequencing reps 1 and 2 merged (at BAM file). Chromsome parts to full chromosome: parts_id parts_start parts_end chrom start end chr1A_part1 0 471304005 chr1A 0 471304005 chr1A_part2 0 122798051 chr1A 471304005 594102056 chr1B_part1 0 438720154 chr1B 0 438720154 chr1B_part2 0 251131716 chr1B 438720154 689851870 chr1D_part1 0 452179604 chr1D 0 452179604 chr1D_part2 0 43273582 chr1D 452179604 495453186 chr2A_part1 0 462376173 chr2A 0 462376173 chr2A_part2 0 318422384 chr2A 462376173 780798557 chr2B_part1 0 453218924 chr2B 0 453218924 chr2B_part2 0 348037791 chr2B 453218924 801256715 chr2D_part1 0 462216879 chr2D 0 462216879 chr2D_part2 0 189635730 chr2D 462216879 651852609 chr3A_part1 0 454103970 chr3A 0 454103970 chr3A_part2 0 296739669 chr3A 454103970 750843639 chr3B_part1 0 448155269 chr3B 0 448155269 chr3B_part2 0 382674495 chr3B 448155269 830829764 chr3D_part1 0 476235359 chr3D 0 476235359 chr3D_part2 0 139317064 chr3D 476235359 615552423 chr4A_part1 0 452555092 chr4A 0 452555092 chr4A_part2 0 292033065 chr4A 452555092 744588157 chr4B_part1 0 451014251 chr4B 0 451014251 chr4B_part2 0 222603248 chr4B 451014251 673617499 chr4D_part1 0 451004620 chr4D 0 451004620 chr4D_part2 0 58852447 chr4D 451004620 509857067 chr5A_part1 0 453230519 chr5A 0 453230519 chr5A_part2 0 256543224 chr5A 453230519 709773743 chr5B_part1 0 451372872 chr5B 0 451372872 chr5B_part2 0 261776885 chr5B 451372872 713149757 chr5D_part1 0 451901030 chr5D 0 451901030 chr5D_part2 0 114179647 chr5D 451901030 566080677 chr6A_part1 0 452440856 chr6A 0 452440856 chr6A_part2 0 165638404 chr6A 452440856 618079260 chr6B_part1 0 452077197 chr6B 0 452077197 chr6B_part2 0 268911281 chr6B 452077197 720988478 chr6D_part1 0 450509124 chr6D 0 450509124 chr6D_part2 0 23083594 chr6D 450509124 473592718 chr7A_part1 0 450046986 chr7A 0 450046986 chr7A_part2 0 286659250 chr7A 450046986 736706236 chr7B_part1 0 453822637 chr7B 0 453822637 chr7B_part2 0 296797748 chr7B 453822637 750620385 chr7D_part1 0 453812268 chr7D 0 453812268 chr7D_part2 0 184873787 chr7D 453812268 638686055 chrUn 0 480980714 chrUn 0 480980714