File script_bwa_UCEs_2022.sh:
In this file, there are a very simple series of commands that allow to create .bam files needed to implement the phasing of UCEs data, that includes the extraction and construction of a SNPs (Single Nucleotide polymorphisms) matrix. This methodology was proposed by Harvey et al. (2016) and includes some modifications by Glaucia Del-Rio (Cornell Laboratory of Ornithology).
The commands use samtools, bwa-mem, and gatk scripts, and does the same processes included in the script phyluce_snp_bwa_multiple_align from the software phyluce (v.1.6). This script is not included in the latest version (v.1.7).
For more information, please read the script!
Bibliography
Faircloth BC. 2015. PHYLUCE is a software package for the analysis of conserved genomic loci. Bioinformatics. doi: 10.1093/bioinformatics/btv646.
Harvey, M. G., Smith, B. T., Glenn, T. C., Faircloth, B. C., Brumfield, R. T. (2016). Sequence Capture versus Restriction Site Associated DNA Sequencing for Shallow Systematics. Systematic Biology, 65(5), 910–924. https://doi.org/10.1093/sysbio/syw036.