Directory structure

• The directory data\ is not included in this github repo because of size, but the content is described below: data/ directory includes:

• data/manifest:
  • GTEx_Analysis_v8_Annotations_SubjectPhenotypesDS.txt
  • GTEx_Analysis_v8_Annotations_SampleAttributesDS.txt
  • participant.tsv
  • GTEx_Portal.csv
• data/counts:
  • GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_tpm_clean.gct

  gunzip GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_tpm.gct.gz
  tail -n +3 GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_tpm.gct > GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_tpm_clean.gct
  

  • GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_reads.gct
• data/vcf:
  • GTEx_Analysis_2017-06-05_v8_WholeExomeSeq_979Indiv_VEP_annot.vcf.gz
  • GTEx_Analysis_2017-06-05_v8_WholeExomeSeq_979Indiv_VEP_annot.vcf.gz.tbi

Generate config file

python generate_gtex_config.py

• The above script outputs: in the directory config/:
  • gtex_tissue_name_config.json: this is the config file for all the tissue names
  • {tissue_name}_config.json (example: Muscle-Skeletal_config.json): this is the config file for each tissue that includes the following list:
    • all_samples
    • females
    • males
    • all_samples_has_rnaseq
    • females_has_rnaseq
    • males_has_rnaseq

Parsing GTEx data

• Script: parse_gtex.py

1. Subset samples from the GTEx TPM or raw count file:

• Example using liver where one specifies the samples to be subsetted via the config file

python parse_gtex.py --data rna --config config/Liver_config.json --gtex_file data/counts/GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_reads_clean.gct --subset_samples_outfile Liver_counts.tsv

• Instead of providing the samples to be subsetted via the config file, you can also provide a sample via --sample or a file with each sample on a row via --samples_file

2. Subset samples from the VCF file:

• Example to subset an individual from the VCF file:

python parse_gtex.py --data dna --sample GTEX-1117F --vcf_file data/vcf/GTEx_Analysis_2017-06-05_v8_WholeExomeSeq_979Indiv_VEP_annot.vcf.gz --subset_samples_outfile GTEX-1117F.vcf