- 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.txtGTEx_Analysis_v8_Annotations_SampleAttributesDS.txtparticipant.tsvGTEx_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.gctGTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_reads.gct
data/vcf:GTEx_Analysis_2017-06-05_v8_WholeExomeSeq_979Indiv_VEP_annot.vcf.gzGTEx_Analysis_2017-06-05_v8_WholeExomeSeq_979Indiv_VEP_annot.vcf.gz.tbi
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
- Script:
parse_gtex.py
- 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
--sampleor a file with each sample on a row via--samples_file
- 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