References

The following software packages are used in this pipeline:

Software	Website	Citation
AWS CLI	https://github.com/aws/aws-cli
BCFtools	https://github.com/samtools/bcftools	doi: 10.1093/gigascience/giab008
BWA	https://github.com/lh3/bwa	doi: 10.48550/arXiv.1303.3997
conda	https://docs.conda.io/en/latest/
fastp	https://github.com/OpenGene/fastp	doi: 10.1093/bioinformatics/bty560
FastQC	https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
GATK4	https://github.com/broadinstitute/gatk
matplotlib	https://matplotlib.org/
MultiQC	https://github.com/ewels/MultiQC	doi: 10.1093/bioinformatics/btw354
pandas	https://pandas.pydata.org/
Python	https://www.python.org/
R	https://www.r-project.org/	R Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria, (2022).
SAMtools	https://github.com/samtools/samtools	doi: 10.1093/gigascience/giab008
Snakemake	https://github.com/snakemake/snakemake	doi: 10.12688/f1000research.29032.1
Somalier	https://github.com/brentp/somalier	doi: 10.1186/s13073-020-00761-2
Tabix	https://github.com/samtools/htslib	doi: 10.1093/gigascience/giab007
VerifyBamID	https://github.com/statgen/verifyBamI	doi: 10.1016/j.ajhg.2012.09.004