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human_male_female

README.rst

human_male_female

These data are created for pipelines that correctly use the ploidy of the X and Y chromosome.

The data can be regenerated reproducible using snakemake.

Files

Files for testing

  • reference: A folder containing a reference genome. With chromosomes 22, X and Y. Fasta index and sequence dictionary files are provided.
  • bwa_index: A folder containing the BWA index files.
  • female: A folder containing the female sample files.
    • female_R1.fastq.gz and female_R2.fastq.gz: fastq files.
    • female.bam and female.bai: Reads aligned to the reference.
  • male: A folder containing the male sample files.
    • Same types of files as female.
  • expected.vcf: The expected genotypes for female and male samples.
  • x_non_par.bed and y_non_par.bed files listing the non-PAR regions for X and Y in reference.fa.

Files involved in test-data creation

  • GRCh38 this folders contains chromosome 22, X and Y downloaded from ensembl. These are the GRCh38 build release 98.
  • extract.bed: The regions from hg38 that were used to create reference.fa.
  • female.ploidy.tsv: ploidy for each chromosome in the female sample.
  • male.ploidy.tsv: idem for male sample.
  • MD5SUMS: checksums to check if data could be recreated reproducably.
  • mutations.vcf: True mutations. Taking ploidy into account. Used to generate the fastq reads for the male and female samples.
  • Snakefile: Workflow to recreate the data
  • Various .py files. used in test data creation.

Test data creation process

  • Chromosome 22, X and Y were downloaded from ensembl. GRCh38 reference genome was used.
  • The chromosomes were concatenated together.
  • extract.bed was used to create a reference.fa.
  • Using translocate.py a version of chromosome Y was created were the masked PAR region was replaced by the sequence of X.
  • Using select_chromosomes and cat a reference_unmasked_y.fa was created.
  • Using male.ploidy.tsv, female.ploidy.tsv, mutations.vcf, reference_unmasked_y.fa and the biotdg programm reads were created for the male and female sample.
  • Using BWA the fastq reads were aligned to reference.fa
  • expected.vcf was created by hand to match the hand-created mutations.vcf. The variants at the end of chromosomes have been removed from expected.vcf