MuSiC original files for testing/ MAF, rois and soo on

Question

[uscUserMut]

Hi all,

I'm new and interested to test music v0.4. Now I have problems to get the same result like in the paper.

"MuSiC: identifying mutational significance in cancer genomes. Dees ND1, Zhang Q, Kandoth C, Wendl MC, Schierding W, Koboldt DC, Mooney TB, Callaway MB, Dooling D, Mardis ER, Wilson RK, Ding L."

I downloaded the same files like it's mentioned in the paper:

Sample data set used in this study

Alignment mapping files for the ovarian cancer cohort, as well as all mutational data in mutation annotation format (MAF) are available at The Cancer Genome Atlas (TCGA) website, http://cancergenome.nih.gov/, via dbGaP. The dbGaP study accession number is phs000178.v1.p1.

But anyway. no chance to get the same results. I have the opportunities or access to get all data, I hopefully think ;), but it doesn't work.

Could anyone help me with the original files or links directly to the original files from that paper?

with best regards

max

[Cyriac Kandoth]

Can you list out the exact data you are using? And which tools in the MuSiC suite are you trying to perform? In "Installation of the MuSiC suite on unsupported Linux distributions" I provide a list of "Datafiles and sample inputs".

[uscUserMut]

at first thanks! i will post it the next days.

Answer 1

[Cyriac Kandoth]

A lot has happened since that publication, so here is an updated list of links to the data used.

Mutations from 316 TCGA OV (ovarian cancer) samples in Mutation Annotation Format (MAF) is from this TCGA publication. To avoid Excel spreadsheet related problems, use the plain-text OV MAF downloadable here.

Alignment mapping (BAM) files are best downloaded from CGHub. If you don't have access to CGHub, it might be simpler to use bmr calc-wig-covg in place of bmr calc-covg. Wiggle files can be found in the Mutation_Packager_Coverage archive from Firehose.

Sample ROI files for use with bmr calc-covg and bmr calc-bmr, can be found in the calc-roi-covg repo.

The datafiles used by MuSiC's cosmic-omim and pfam tools are downloadable from here.