Computational Biologist
Please visit this page once you have done things necessary here: https://mskcc.github.io/on-boarding/
The best place to start is to learn more about MSK-ACCESS and for that please read the paper:
Learn more about the current collapsing method Marianas
Learn more about the Quality Control V1
Understand the updated version for the above using these Quality Control V2
Learn about ACCESS Data analysis scripts that help with downstream analysis
Learn about IGV for viewing BAM files to distinguish real variants from artifacts
Below are resources that would be handy for you to learn more about all the tools described in the paper.
Project Management
MSK-ACCESS
CMO-CH
CMO Cell-Free Informatics (CCI)
Functional Resources
MSK-ACCESS V1 (Marianas)
CCI organization on Github
cBioPortal DMP data
Quality Control for ACCESS V1
Downstream analysis of ACCESS Data
Fingerpriting using Biometrics
High Performance Computing
Nucleo (Fgbio)
Quality Control for ACCESS V2
Path's to know
CMO-ACCESS
Data on JUNO for CMO-ACCESS samples
BAM
/juno/work/access/production/data/bams/{cmo_patient_id}/{cmo_sample_id}/current/
Small Variant (SNV’s/INDEL’s)
/juno/work/access/production/data/small_variants/{cmo_patient_id}/{cmo_sample_id}/current/
Microsatellite Instability(MSI)
/juno/work/access/production/data/microsatellite_instability/{cmo_patient_id}/{cmo_sample_id}/current/
Structural Variant (SV)
/juno/work/access/production/data/structural_variants/{cmo_patient_id}/{cmo_sample_id}/current/
Copy Number Variants (CNV)
/juno/work/access/production/data/copy_number_variants/{cmo_patient_id}/{cmo_sample_id}/current/
Resources
NYS validation data
/work/access/production/runs/NYS_validation/current
CMO-ACCESS
/work/access/production/
/work/access/production/resources/
CMO-CH
/work/ch/
Berger Lab
/work/bergerm1/bergerlab
Details of CMO ACCESS Resources
admie
- Files used for microsatellite instability detection tool ADMIE for MSK-ACCESScosmic
- VCF file of cosmic used in MSK-ACCESS workflowsdbSNP
- VCF file of dbSNP used in MSK-ACCESS workflowsexac
- VCF file of ExAC used in MSK-ACCESS workflowsmills-and-1000g
- VCF file of mills-and-1000g used in MSK-ACCESSreference
- reference genome file used in MSK-ACCESS workflowstools
- general packages used in MSK-ACCESS workflowsmsk-access
- Data-specific resources for MSK-ACCESS workflows. This includes the following:hiseq4000_curated_duplex_bams_dmp
- curated DMP duplex BAMS from HiSeq 4000novaseq_curated_simplex_bams_dmp
- curated DMP simplex BAM from NovaSeq.hiseq4000_curated_simplex_bams_dmp
- curated DMP simplex BAM from HiSeq 4000novaseq_curated_standard_bams_dmp
- curated DMP standard BAM from NovaSeqhiseq4000_curated_standard_bams_dmp
- curated DMP standard BAM from HiSeq 4000novaseq_curated_unfiltered_bams_dmp
- curated DMP unfiltered BAM from NovaSeqhiseq4000_curated_unfiltered_bams_dmp
- curated DMP unfiltered BAM from HiSeq 4000novaseq_unmatched_normal_plasma_duplex_bams_dmp
- DMP unmatched normal plasma duplex BAM from NovaSeqhiseq4000_unmatched_normal_plasma_duplex_bams_dmp
- DMP unmatched normal plasma duplex BAM from HiSeq 4000novaseq_unmatched_normal_plasma_standard_bams_dmp
- DMP unmatched normal plasma standard BAM from NovaSeqhiseq4000_unmatched_normal_plasma_standard_bams_dmp
- DMP unmatched normal plasma standard BAM from HiSeq 4000novaseq_curated_duplex_bams_dmp
- curated DMP duplex BAMS from NovaSeqregions_of_interest
- Different interval files describing regions of interest for MSK-ACCESS assay
If we can justify adding data/tools to the above-mentioned location please contact Ronak Shah.
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