jburos
commented
7 years ago Hi @js2dark - This is a great use case for cohorts; we are happy to help.
We have some worked examples of how to combine VCFs & clinical data into a cohort object. For example, an example using TCGA data, with some explanatory text, which references an earlier example for creating a cohort with clinical data only.
In all of these examples, the basic approach is the same: you loop over the units in your cohort (ie patients), creating a Patient object for each one. You then pass this list of Patients to create the Cohort object.
I will say, neither of the examples above includes the use of BAMs; to include these you will want to (when creating a Patient), also create Samples for each of your samples (tumor &/or normal). Then these Sample objects get included when creating the Patient.
For example:
normal_sample = Sample(
is_tumor=False,
bam_path_dna=bam_path_dna_normal)
tumor_sample = Sample(
is_tumor=True,
bam_path_dna=bam_path_dna_tumor,
bam_path_rna=bam_path_rna_tumor,
kallisto_path=kallisto_path,
cufflinks_path=cufflinks_path)These are then passed to the Patient object when it is instantiated:
patient = Patient(id=patient_id,
benefit=row["is_benefit"],
os=row["OS in days"],
pfs=row[pfs_col], # Depends in RECIST choice
deceased=row["is_deceased"],
progressed=row["is_progressed"],
progressed_or_deceased=row["is_progressed_or_deceased"],
hla_alleles=row["hla_allele_list"],
vcf_paths=snv_vcf_paths,
normal_sample=normal_sample, # <- here
tumor_sample=tumor_sample, # <- and here
additional_data=row.to_dict())NB: these examples are taken from the code we used recently to analyze some data from a cohort. Including that code here as possibly a more complete example, although beware it was using an earlier version of cohorts so some options may have changed since then.
Hope this gives you a good starting point. Feel free to get in touch if you run into sticky points or to give feedback on the documentation -- admittedly we need to do more on that front & to make these examples easier to find.
js2dark
tavinathanson
Hello, I'm fairly new to python and I've been trying to use the cohorts library to mainly calculate neoantigens in my tumor samples. I have each tumor's processed BAM and VCF files but I'm having a difficult time trying to combine them into creating a cohort to proceed to counting neoantigens. If there is any step by step manual to creating a cohort, I would greatly appreciate if you could share it Thank you and hope to hear from you soon