Humble E, Stoffel MA, Dicks K, Ball AD, Gooley RM, Chuven J, Pusey R, Al Remeithi M, Koepfli KP, Pukazhenthi B, Senn H, Ogden R (2023) Conservation management strategy impacts inbreeding and mutation load in scimitar-horned oryx. PNAS. 120, 18. https://doi.org/10.1073/pnas.2210756120.
This repository contains the scripts used for aligning reads and calling SNPs for resequenced individuals, running ANGSD, calling ROH, polarising alleles, annotating variants and running GONe.
Detailed workflows for each stage of the pipeline are stored under /workflows.
Some of the bash scripts are highly parallelised and call additional scripts inside the /scripts directory.
For downstream analysis and visualisation of outputs, please see github repository SHO_roh_load_2022.
Read alignment
1.1_cutadapt_NS.sh
1.2_IndexRef.sh
2.0_AlignReads_HS.sh
2.0_AlignReads_NS.sh
2.1_SortSam.sh
2.2_ReadGroups_HS.sh
2.2_ReadGroups_NS.sh
2.3_MergeSam_NS.sh
2.4_MarkDups_HS.sh
2.4_MarkDups_NS.sh
2.5_BamCov.sh
2.6_HS_DS.sh
2.7_DownsampleBams.sh
2.8_IndexBams.sh
SNP calling
3.0_SeqDict.sh
3.1_run_HapCaller_DS.sh
3.1_run_HapCaller_NS.sh
3.2_GGVCFs_DS_NS.sh
3.3_CatVariants.sh
ANGSD analysis
4.0_angsd.sh
4.1_run_angsd_pop.sh
4.2_angsd_ld.sh
4.3_run_angsd_ld_pop.sh
4.4_run_angsdHet.sh
4.5_run_realSFS.sh
4.6_run_SFS_pop.sh
4.7_run_doThetas_pop.sh
5.0_PCAngsd.sh
5.1_NGSadmix.sh
Polarisation and variant annotation
6.0_align_sp.sh
6.1_SortSam.sh
6.2_MergeSam.sh
6.3_doFasta.sh
6.4_vcf_to_bed.sh
6.5_format_ancestral_alleles.sh
7.0_SNPeff.sh
7.1_VEP.sh
Ne analysis
8.0_GONe.sh
Sequencing reads required to run the pipeline are available at the European Nucleotide Archive (https://www.ebi.ac.uk/ena/browser) under study accession PRJEB37295.
Genome assembly and RefSeq annotation used in the pipeline (GCF_014754425.2) are available here.