search

xjtu-omics / msisensor-pro

Microsatellite Instability (MSI) detection using high-throughput sequencing data.
Other
93 stars 20 forks source link

Is it possible to adapt this tool for running on VCF/MAF? #3

Closed jjgao closed 4 years ago

jjgao commented 4 years ago

For published studies, we usually don't have access to BAM. I am wondering if it is possible to calculate MSI scores just based on called mutations?

PengJia6 commented 4 years ago

For published studies, we usually don't have access to BAM. I am wondering if it is possible to calculate MSI scores just based on called mutations?

I am sorry, It is not available for MSI calling based on VCf/MAF in current version. Thanks for your suggestion. We will explore the prosibility of you mentioned in the future, but the key problem is that researchers may get different VCF from one same bam file, because of the different usage of softwares and parameters.

jjgao commented 4 years ago

@PengJia6 thanks for the response! It would be great if we will be able to use it on MAF. We are very interested in calculating msi scores for all samples in cBioPortal, but we don't have access to most of the BAM files. https://github.com/cBioPortal/datahub/issues/1043

jjgao commented 4 years ago

Another related question: do you happen to have msi scores for all tcga samples? If so, we would be very interested in integrating them into cBioPortal.

PengJia6 commented 4 years ago

Another related question: do you happen to have msi scores for all tcga samples? If so, we would be very interested in integrating them into cBioPortal.

I am sorry we do not have msi scores for all tcga samples. We just called the sample in in colorectal cancer (CRC), stomach adenocarcinoma (STAD), and uterine corpus endometrial carcinoma (UCEC) in TCGA and you can find the results in our research paper.

PengJia6 commented 4 years ago

@PengJia6 thanks for the response! It would be great if we will be able to use it on MAF. We are very interested in calculating msi scores for all samples in cBioPortal, but we don't have access to most of the BAM files. cBioPortal/datahub#1043

Thanks for you advance, we will do it in the future.

jjgao commented 4 years ago

Thanks, @PengJia6!

PengJia6 commented 3 years ago

@jjgao Hi, we have launched new software MSIsensor-RNA for MSI detection with RNA-seq data. If you do not have access to bam files, it is a choice for you to try with RNA expression data, like FPKM.