Personal Genomes

This package creates personal genomes for alignment of samples with known genetic variation, converts coordiantes of files aligned to the personal genome back to GRCh38, and counts alleles of the known variants.

Dependencies

Personal Genomes Requires

- python (>=3.9.12)
- numpy (>=1.20.3)
- pysam (>=0.15.3)

Usage

1. Use write_genome_and_all_vcf.py to create a personal genome.
2. Align fasta files to the personal genome.
3. Use convert_to_hg38.py to convert SAM file from personal genome coordinates to GRCh38 coordinates.
4. Sort reads in the GRCh SAM file.
5. Use count_alleles.py to count alleles of known variants in the sorted SAM file.