Closed LeeTL1220 closed 9 years ago
Please note that the collapsing will only happen when output is TCGA MAF. Please note that the current design could be leveraged for more versatile functionality in the future.
Collapsing will happen in the TCGA MAF output.
Now for a checklist:
Unit tests:
For the second Oncotator run in the pipeline.... As of this writing, the relevant task config in FH will be:
input_format: TCGAMAF
output_format: TCGAMAF
additional_options: --log_name oncotator_firehose.log --prepend --infer-onps -c /xchip/cga/reference/annotation/db/tx_exact_uniprot_matches.txt --collapse-number-annotations
No other task config parameters should be changed from standard (incl. no venv changes)
Here are commands that, as of this writing, I believe to work:
# Step 1 VCF to MAF (pre-oxoG filter)
oncotator -v -i VCF -o TCGAMAF --collapse-filter-cols --skip-no-alt test/testdata/m2_support/phasingExample.vcf ~/broad_oncotator_configs/phasingTest.vcf.maf.annotated hg19 --db-dir ~/dbdir_current -c ~/broad_oncotator_configs/tx_exact_uniprot_matches.AKT1_CRLF2_FGFR1.txt --log_name ~/broad_oncotator_configs/step1_oncotator.log --prepend
# Step 2 TCGA MAF to TCGA MAF with ONP and value collapse (post-oxoG filter)
oncotator -v -i TCGAMAF -o TCGAMAF ~/broad_oncotator_configs/phasingTest.vcf.maf.annotated ~/broad_oncotator_configs/test_reannotate.maf.annotated --infer-onps -c ~/broad_oncotator_configs/tx_exact_uniprot_matches.AKT1_CRLF2_FGFR1.txt hg19 --db-dir /home/lichtens/dbdir_current --prepend --collapse-number-annotations --log_name ~/broad_oncotator_configs/step2_oncotator.log
@kcibul Though this issue is closed, there is useful information for creating FH task configs/modules.
Please see issue #325 for more details. The first part of the OxoG filter fixes (issue #325 ) includes:
This issue will include the collapsing of number output fields as specified by user (with appropriate default). Particularly, this is useful for when we have DNPs and downstream tools expect a single number.