Open itigupta2429 opened 5 days ago
Hi @itigupta2429,
If you are looking to assign COSMIC signatures to a set of samples then you will want to use cosmic_fit. Please reach out if you have any additional questions.
Hi @mdbarnesUCSD,
I am using the following command:
Analyze.cosmic_fit(
samples="./test/BRCA_vcf",
output="test_vcf",
input_type="vcf",
genome_build="GRCh37",
context_type="96",
export_probabilities_per_mutation="TRUE",
export_probabilities="TRUE"
)
After running this, I expected to find a file that contains mutation-level assignments, indicating which SBS signature is linked to each mutation from the input VCF. However, after thoroughly reviewing all the output files, I can't locate any file that provides this information.
Could you please clarify where this file should be generated or if there’s an additional step required to obtain mutation-wise signature assignments?
Thanks for your help!
Thanks for clarifying. It seems that you would like to export the probabilities per mutation file. I suspect the issue is that you are currently passing the string "TRUE". Please try again using the boolean True as shown below.
Analyze.cosmic_fit(
samples="./test/BRCA_vcf",
output="test_vcf",
input_type="vcf",
genome_build="GRCh37",
context_type="96",
export_probabilities_per_mutation=True,
export_probabilities=True
)
Please let us know if this resolves the issue. Thanks!
Thanks for your quick response!
With the earlier code as well I was getting the probabilities per mutation file (inside: BRCA_vcf/output/vcf_files/SNV
)
The folder contains chromosome wise files; and If I see one file it contains information like:
PD4120a 10 71718 N:GA[T>A]CA 1
PD4120a 10 115370 N:AC[T>A]AC -1
PD4120a 10 117751 N:CT[C>A]AG -1
PD4120a 10 212461 U:TT[C>T]AG 1
PD4120a 10 247953 U:AC[C>G]TG 1
PD4120a 10 311033 N:AC[C>T]GG -1
PD4120a 10 369240 T:GG[C>G]TC 1
PD4120a 10 387315 T:CT[C>G]AG 1
PD4120a 10 442142 T:TT[C>G]AA 1
PD4120a 10 471214 T:AG[C>T]GG 1
PD4120a 10 484448 U:CT[C>G]AA -1
PD4120a 10 520650 T:CT[C>G]TT 1
PD4120a 10 646938 T:CT[C>T]AT 1
PD4120a 10 657996 U:CT[C>T]CC -1
I have a couple of questions regarding this:
Hi Team, I had a query. I would like to extract which mutations are assigned to which SBS signature for each sample. Is there a way I can do that? I am using sigProfiler Assignment. Thanks in advance