v12-filter-mtp tables

[ewafula]

Purpose/implementation Section

What scientific question is your analysis addressing?

Update filter-mtp-tables module for v12 MTP tables

What was your approach?

• updated module to filter and update MTP tables based on the Open Targets Platform Targets and Disease/Phenotype annotations.
• change input MTP tables to be downloaded from the s3 bucket and written to scratch for subsequent upload back to the s3 bucket
• include filtering of MTP methylation summary tables

What GitHub issue does your pull request address?

• Updated filter-mtp-tables module ticket-tracker-OPC#511

Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.

Which areas should receive a particularly close look?

• code updates in both bash and Rmd scripts
• results files - both the filtered and updated MTP tables in scratch/ folder and filtered out ESNGs and affected sample_ids in the results/ folder

Is there anything that you want to discuss further?

• Will require large memory OpenPendcan EC2 instance

Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?

Results

What types of results are included (e.g., table, figure)?

Tables

What is your summary of the results?

• ../../scratch/gene-level-cnv-consensus-annotated-mut-freq.jsonl.gz
• ../../scratch/gene-level-cnv-consensus-annotated-mut-freq.tsv.gz
• ../../scratch/gene-level-snv-consensus-annotated-mut-freq.jsonl.gz
• ../../scratch/gene-level-snv-consensus-annotated-mut-freq.tsv.gz
• ../../scratch/gene-methyl-beta-values-summary.jsonl.gz
• ../../scratch/gene-methyl-beta-values-summary.rds
• ../../scratch/gene-methyl-beta-values-summary.tsv.gz
• ../../scratch/isoform-methyl-beta-values-summary.jsonl.gz
• ../../scratch/isoform-methyl-beta-values-summary.rds
• ../../scratch/isoform-methyl-beta-values-summary.tsv.gz
• ../../scratch/long_n_tpm_mean_sd_quantile_gene_wise_zscore.jsonl.gz
• ../../scratch/long_n_tpm_mean_sd_quantile_gene_wise_zscore.tsv.gz
• ../../scratch/long_n_tpm_mean_sd_quantile_group_wise_zscore.jsonl.gz
• ../../scratch/long_n_tpm_mean_sd_quantile_group_wise_zscore.tsv.gz
• ../../scratch/putative-oncogene-fused-gene-freq.jsonl.gz
• ../../scratch/putative-oncogene-fused-gene-freq.tsv.gz
• ../../scratch/putative-oncogene-fusion-freq.jsonl.gz
• ../../scratch/putative-oncogene-fusion-freq.tsv.gz
• ../../scratch/variant-level-snv-consensus-annotated-mut-freq.jsonl.gz
• ../../scratch/variant-level-snv-consensus-annotated-mut-freq.tsv.gz
• results/gene-level-cnv-consensus-annotated-mut-freq_dropped_ensg.tsv.gz
• results/gene-level-snv-consensus-annotated-mut-freq_dropped_ensg.tsv.gz
• results/gene-methyl-beta-values-summary_dropped_ensg.tsv.gz
• results/isoform-methyl-beta-values-summary_dropped_ensg.tsv.gz
• results/long_n_tpm_mean_sd_quantile_gene_wise_zscore_dropped_ensg.tsv.gz
• results/long_n_tpm_mean_sd_quantile_group_wise_zscore_dropped_ensg.tsv.gz
• results/putative-oncogene-fused-gene-freq_dropped_ensg.tsv.gz
• results/putative-oncogene-fusion-freq_dropped_ensg.tsv.gz
• results/variant-level-snv-consensus-annotated-mut-freq_dropped_ensg.tsv.gz
• 01-filter-mtp-tables-for-current-gencode.nb.html

Reproducibility Checklist

• The dependencies required to run the code in this pull request have been added to the project Dockerfile.
• This analysis has been added to continuous integration.

Documentation Checklist

• This analysis module has a README and it is up to date.
• This analysis is recorded in the table in analyses/README.md and the entry is up to date.
• The analytical code is documented and contains comments.

[atlas4213]

The logic looks good and the code successfully ran. Approving

[zzgeng]

Looking good to me! Approving!

[jharenza]

@ewafula can you use below the general glial neuronal tumor IDs for each of these? thanks

Diffuse leptomeningeal glioneuronal tumor	MONDO_0016729	MONDO_0016729	NCIT_C4747
Extraventricular neurocytoma MONDO_0016729	MONDO_0016729	NCIT_C4747