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:

  • Brannon, A. R. et al. Enhanced specificity of clinical high-sensitivity tumor mutation profiling in cell- free DNA via paired normal sequencing using MSK-ACCESS. Nat Commun 12, 3770 (2021).

• Learn more about the current collapsing method Marianas

• Learn more about the new collapsing (Nucleo) method using Fgbio

• 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

Assay/Team	Link to the tool
MSK-ACCESS	Link to AirTable
CMO-CH	Link to AirTable
CMO Cell-Free Informatics (CCI)	https://clickup.com/ - Request access once you have your msk email id

Functional Resources

Assay/Purpose/Team/Tool	URL
MSK-ACCESS V1 (Marianas)	https://github.com/mskcc/ACCESS-Pipeline
CCI organization on Github	https://github.com/msk-access
cBioPortal DMP data	InternalLink: https://github.mskcc.org/knowledgesystems/dmp-2022
Quality Control for ACCESS V1	Access Quality Control (v1)
Downstream analysis of ACCESS Data	https://cmo-ci.gitbook.io/cmo-access-data-analysis/
Fingerpriting using Biometrics	https://cmo-ci.gitbook.io/biometrics/
High Performance Computing	https://mskcchpc.org/
Nucleo (Fgbio)	https://github.com/msk-access/nucleo
Quality Control for ACCESS V2	https://cmo-ci.gitbook.io/access-quality-control-v2/

Path's to know

CMO-ACCESS

Data on JUNO for CMO-ACCESS samples

Analysis Type	JUNO Location
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

Resource Type	JUNO Location
NYS validation data	/work/access/production/runs/NYS_validation/current
CMO-ACCESS	/work/access/production/
CMO-ACCESS Resources	/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-ACCESS

• cosmic - VCF file of cosmic used in MSK-ACCESS workflows

• dbSNP - VCF file of dbSNP used in MSK-ACCESS workflows

• exac - VCF file of ExAC used in MSK-ACCESS workflows

• mills-and-1000g - VCF file of mills-and-1000g used in MSK-ACCESS

• reference - reference genome file used in MSK-ACCESS workflows

• tools - general packages used in MSK-ACCESS workflows

• msk-access - Data-specific resources for MSK-ACCESS workflows. This includes the following:

  • hiseq4000_curated_duplex_bams_dmp - curated DMP duplex BAMS from HiSeq 4000

  • novaseq_curated_simplex_bams_dmp - curated DMP simplex BAM from NovaSeq.

  • hiseq4000_curated_simplex_bams_dmp - curated DMP simplex BAM from HiSeq 4000

  • novaseq_curated_standard_bams_dmp - curated DMP standard BAM from NovaSeq

  • hiseq4000_curated_standard_bams_dmp - curated DMP standard BAM from HiSeq 4000

  • novaseq_curated_unfiltered_bams_dmp - curated DMP unfiltered BAM from NovaSeq

  • hiseq4000_curated_unfiltered_bams_dmp - curated DMP unfiltered BAM from HiSeq 4000

  • novaseq_unmatched_normal_plasma_duplex_bams_dmp - DMP unmatched normal plasma duplex BAM from NovaSeq

  • hiseq4000_unmatched_normal_plasma_duplex_bams_dmp - DMP unmatched normal plasma duplex BAM from HiSeq 4000

  • novaseq_unmatched_normal_plasma_standard_bams_dmp - DMP unmatched normal plasma standard BAM from NovaSeq

  • hiseq4000_unmatched_normal_plasma_standard_bams_dmp - DMP unmatched normal plasma standard BAM from HiSeq 4000

  • novaseq_curated_duplex_bams_dmp - curated DMP duplex BAMS from NovaSeq

  • regions_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.