Hi Solomon,
The file should contain the term ‘oxoG’ these are the results of running oxoG at some intermediate step between the workflow results and the final consensus, before or after bias-filtering I’m not sure. The ICGC seems to contain only the workflow results and the final consensus, but not these steps. I check this by downloading the fill PCAWG export from the REST API, for a particular donor I get these files:
Aligned Reads.Normal - blood derived.8d35619347952f08d81bcd78beb4e64e.bam
Aligned Reads.Primary tumour - solid tissue.f665fc5c67b645d3038770c49c02fb02.bam
CNSM.Primary tumour - solid tissue.fc876f66-ff0d-f338-e040-11ac0d485162.dkfz-copyNumberEstimation_1-0-189-hpc-fix.1508262003.somatic.cnv.vcf.gz
CNSM.Primary tumour - solid tissue.fc876f66-ff0d-f338-e040-11ac0d485162.svcp_1-0-4.20150212.somatic.cnv.vcf.gz
SGV.Primary tumour - solid tissue.fc876f66-ff0d-f338-e040-11ac0d485162.broad-snowman.20150918.germline.indel.vcf.gz
SGV.Primary tumour - solid tissue.fc876f66-ff0d-f338-e040-11ac0d485162.dkfz-indelCalling_1-0-132-1.20150611.germline.indel.vcf.gz
SGV.Primary tumour - solid tissue.fc876f66-ff0d-f338-e040-11ac0d485162.dkfz-snvCalling_1-0-132-1.20150611.germline.snv_mnv.vcf.gz
SSM.Primary tumour - solid tissue.fc876f66-ff0d-f338-e040-11ac0d485162.broad-mutect-v3.20160222.somatic.snv_mnv.vcf.gz
SSM.Primary tumour - solid tissue.fc876f66-ff0d-f338-e040-11ac0d485162.broad-snowman.20150918.somatic.indel.vcf.gz
SSM.Primary tumour - solid tissue.fc876f66-ff0d-f338-e040-11ac0d485162.consensus.20160830.somatic.snv_mnv.vcf.gz
SSM.Primary tumour - solid tissue.fc876f66-ff0d-f338-e040-11ac0d485162.consensus.20161006.somatic.indel.vcf.gz
SSM.Primary tumour - solid tissue.fc876f66-ff0d-f338-e040-11ac0d485162.dkfz-indelCalling_1-0-132-1.20150611.somatic.indel.vcf.gz
SSM.Primary tumour - solid tissue.fc876f66-ff0d-f338-e040-11ac0d485162.dkfz-snvCalling_1-0-132-1.20150611.somatic.snv_mnv.vcf.gz
SSM.Primary tumour - solid tissue.fc876f66-ff0d-f338-e040-11ac0d485162.MUSE_1-0rc-vcf.20150918.somatic.snv_mnv.vcf.gz
SSM.Primary tumour - solid tissue.fc876f66-ff0d-f338-e040-11ac0d485162.svcp_1-0-4.20150212.somatic.indel.vcf.gz
SSM.Primary tumour - solid tissue.fc876f66-ff0d-f338-e040-11ac0d485162.svcp_1-0-4.20150212.somatic.snv_mnv.vcf.gz
StGV.Primary tumour - solid tissue.fc876f66-ff0d-f338-e040-11ac0d485162.broad-snowman.20150918.germline.sv.vcf.gz
StGV.Primary tumour - solid tissue.fc876f66-ff0d-f338-e040-11ac0d485162.embl-delly_1-0-0-preFilter.20150611.germline.sv.vcf.gz
StSM.Primary tumour - solid tissue.fc876f66-ff0d-f338-e040-11ac0d485162.broad-dRanger.20150918.somatic.sv.vcf.gz
StSM.Primary tumour - solid tissue.fc876f66-ff0d-f338-e040-11ac0d485162.broad-dRanger_snowman.20150918.somatic.sv.vcf.gz
StSM.Primary tumour - solid tissue.fc876f66-ff0d-f338-e040-11ac0d485162.broad-snowman.20150918.somatic.sv.vcf.gz
StSM.Primary tumour - solid tissue.fc876f66-ff0d-f338-e040-11ac0d485162.embl-delly_1-0-0-preFilter.20150611.somatic.sv.vcf.gz
StSM.Primary tumour - solid tissue.fc876f66-ff0d-f338-e040-11ac0d485162.svfix2_4-0-12.20160213.somatic.sv.vcf.gz
As you can see these are the BAM files, the workflow results and the consensus. The files I need where available in GNOS and listed in the file:
variant_call_entries_with_broad_oxog_filter_applied.txt
Without them I cannot test the results of the OxoG filter, since I need this as a comparison, or the Consensus, since I need them as input.
Best
Miguel