The data used in this analysis were previously published in Shao et al., (2020). You can dowload the FASTQ files from the National Center for Biotechnology Information Short Read Archive (NCBI SRA) under BioProject accession PRJNA574141.
There are a lot of very similar files in this directory. Usually, I try to make general scripts so that they can be recycled for nearly identical scripts. The script filter_snps_and_make_wide_format.R is a good example of this. In the case of downsampling, I used different subdirectories for some of the analyses so the only difference might be the path to the working directory. The input files might also differ slightly. For example, in filter_with_vcftools_2fold.sh (as well as the 4-fold and 8-fold versions), the input file name vcf_list_new_2fold.txt was just called vcf_list_new.txt in the directory, but has been renamed here so they won't conflict with each other.
- Trimmed FASTQ files were downsampled using downsampling_2fold.sh, downsampling_4fold.sh, and downsampling_8fold.sh.
- Downsampled FASTQ files were aligned to the NWR genome using run_bwa_downsampling_2fold.sh, run_bwa_downsampling_4fold.sh, and run_bwa_downsampling_8fold.sh.
- BAM files were indexed using make_bam_indicies.sh.
- SNP calling was done (with samtools mpileup/bcftools call) using scythe_mpileup_downsampled_2fold.sh, scythe_mpileup_downsampled_4fold.sh, and scythe_mpileup_downsampled_8fold.sh.
- VCF files were filtered (10% missing data, bi-allelic sites only, minimum of 6 reads) using filter_with_vcftools_2fold.sh, filter_with_vcftools_4fold.sh, and filter_with_vcftools_8fold.sh.
Shao, M., Haas, M., Kern, A., and Kimball, J. (2020) Identification of single nucleotide polymorphism markers for population genetic studies in Zizania palustris L. Conservation Genetics Resources 12, 451-455