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VanLoo-lab / ascat

ASCAT R package
https://www.mdanderson.org/research/departments-labs-institutes/labs/van-loo-laboratory/resources.html#ASCAT
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logR and BAF from tumour only #120

Closed haeflis628 closed 1 year ago

haeflis628 commented 1 year ago

Hi Is it possible to get logR and BAF of sequencing data if only tumour samples available with the ascat.prepareHTS () function? Thank you in advance and best regards Simon

tlesluyes commented 1 year ago

Hi Simon,

We do require T/N pairs for now. We have a plan to derive logR and BAF for tumour samples only but such a method would only be available in a few months.

Cheers,

Tom.

haeflis628 commented 1 year ago

Thank you for your quick response. Just to be sure running the analysis with a germline bam file of another patient would be wrong right? Best regards and thanks again. Simon

On Fri, Oct 21, 2022 at 1:47 PM tlesluyes @.***> wrote:

Hi Simon,

We do require T/N pairs for now. We have a plan to derive logR and BAF for tumour samples only but such a method would only be available in a few months.

Cheers,

Tom.

— Reply to this email directly, view it on GitHub https://github.com/VanLoo-lab/ascat/issues/120#issuecomment-1286916752, or unsubscribe https://github.com/notifications/unsubscribe-auth/A3XX77VZRS2MI4RIRJS56ILWEKGHFANCNFSM6AAAAAARLD4E2Q . You are receiving this because you authored the thread.Message ID: @.***>

tlesluyes commented 1 year ago

Hi Simon,

Correct. ASCAT uses heterozygous SNPs and those are different from one patient to another. Using an unmatched normal would break the process.

Cheers,

Tom.

MAlinkous commented 1 year ago

Hi, I want to use Software SGZ (https://github.com/jsunfmi/SGZ) to get somatic variation results form my tumor-only WES data and a CNA file is needed for input besides variation data. Your software is recommended by SGZ for generation of CAN file. Buct after reading your manual and Issues on GitHub, I still have no clue on how to generate a CAN file from tumor-only WES data. I am confused because ASCAT is recommand to get CNA file on a tumor-only based software, but normal samples are need for use of ASCAT. Is there any solution for generation of a CNA file (genotype prediction not need) ?

Thanks for your reading

tlesluyes commented 1 year ago

Hi @MAlinkous,

ASCAT does require T/N pairs for processing sequencing (WES included) data but can do tumour-only analyses using SNP arrays.

Cheers,

Tom.