I wanted to look at the full list of mutations in the output for the provided minimal maf file. However, when I did this by relaxing the q-value threshold it resulted in errors in handling mutations with chromosome "MT" or anything starting with "GL" (these are in the MAF file). I have included an error message below:

Error in .getOneSeqFromBSgenomeMultipleSequences(x, name, start, NA, width, : sequence chrGL000205.1 not found Calls: cbind ... lapply -> FUN -> .getOneSeqFromBSgenomeMultipleSequences)

Collin

Hello,

I tried to get the MAF file using the Google Drive link, but I get a Not Found error (404).

Thanks

When I run the code, it gives back an error here. No ___tmp.tsv file in the directory. No such file has been created before. Can you please help me??

Thank you!

Hi,

It seems like your googledrive link is down. Could you provide another link ?

Access to the full mutational data can be obtained here: https://googledrive.com/host/0B1tQDSL9FmNLTmo1dl9SRF9USUE
Note, file is ~1.8G in size. md5sum: 94a3538afdbfbc8b52c75914c60c9f78

Thank you for this work, it's great !

Kind regards,

Y. Boursin, Gustave Roussy

Hi. Can this program be used in GRCh38 data?

We tried to run this tool for our Lung genome analysis. We used standard MAF with 32 columns and this is not working. Can you please let know which columns in MAF are necessary to run this analysis?
We will appreciate your help !
Thanks,
Ashiq

Question:
I was wondering for the publication_hotspots.vcf is this for the 2015 paper only (https://pubmed.ncbi.nlm.nih.gov/26619011/)? And if so, is there a vcf/bed files for the 2017 paper (https://aacrjournals.org/cancerdiscovery/article/8/2/174/6249/Accelerating-Discovery-of-Functional-Mutant) available somewhere?

Files:
https://github.com/taylor-lab/hotspots/blob/source_Aug2018/publication_hotspots.vcf
https://github.com/taylor-lab/hotspots/blob/master/publication_hotspots.bed

Hi,

Would it be possible to get genomic coordinates of sites in https://github.com/taylor-lab/hotspots/blob/master/true_positive_hotspots.txt maybe maf or vcf format?

Thanks,
Rajesh

I've attempted to run the following code from README:

/hotspot_algo.R --input-maf=minimalist_test_maf.txt --rdata=hotspot_algo.Rdata --gene-query=genes_of_interest.txt --output-file=testrun_sig_hotspots.txt

and I've got this:

Reading in MAF...
Prepping MAF for analysis ...
... Ignoring non-SNP mutations
... Making bed file
... Getting regions
Error: The requested fasta database file (/ifs/depot/assemblies/H.sapiens/GRCh37/gr37.fasta) could not be opened. Exiting!
... Adding trinucs (normalized to start from C or T)
... Writing to ___temp_maf-tri.tm
... Cleaning up

It seems that the script require a giant gr37.fasta instead of multiple files. How could I fix this?

hi:
i got a error when try to use minimalist_test_maf.txt and filter-centerbias=TRUE

Annotating mutation calling center bias...
data frame with 0 columns and 0 rows
Error in names(x) <- value :
'names' attribute [7] must be the same length as the vector [0]
Calls: cbind ... eval -> annotate.center.bias -> colnames<- -> colnames<-
Execution halted

Access to the full mutational data can be obtained here: https://drive.google.com/open?id=0B1tQDSL9FmNLTmo1dl9SRF9USUE
I tried to open the link using my Google account, but I encountered an error. Could you please grant me permission to access the file?

Hi,

I'm getting an error originating from the amino acid length being NA.

It looks like from looking at the internals of the code that you assume the "Protein_position" column should be something like "position/length", where "position" is the amino acid position of the mutation and "length" is the total length of the protein. Despite a MAF file from TCGA containing a "Protein_position" column, it only contains the "position" part and not anything related to the protein length.

Collin

Hello,

Thank you developing this useful tool. I was able to run the example maf file successfully by downloading the GRCH37 fasta file however when I try to run the hotspot script by giving the my own data:
./hotspot_algo.R --input-maf=data_ext_mut.maf --rdata=hotspot_algo.Rdata --output-file=data_hotspot.maf

I get the following log and error:

No q-value entered. Using default q-value cut-off, 0.01
Using: HOMOPOLYMER_FILTER

Reading in MAF...
Prepping MAF for analysis ...
... Reducing MAF to protein-coding substitutions
... Re-annotating substitutions
... Removing putative germline SNPs based on ExAC r0.2
... Removing unexpressed genes
... Ignoring non-SNP mutations
... Making bed file
... Getting regions
WARNING. chromosome (GL000219.1) was not found in the FASTA file. Skipping.
WARNING. chromosome (GL000219.1) was not found in the FASTA file. Skipping.
WARNING. chromosome (GL000193.1) was not found in the FASTA file. Skipping.
... Adding trinucs (normalized to start from C or T)
... Writing to ___temp_maf-tri.tm
... Cleaning up

Finished prepping MAF!
Running algorithm...
Error in rep(1, aa.length - length(pval)) : invalid 'times' argument
Calls: lapply -> lapply -> FUN
Execution halted

Further investigation of the code seems to indicate the error is from the binom.test_snp function but I am not sure why I'm getting it. How do I got about identifying part that seems to break and resolve this issue?

Thanks,
Krutika

hi sir:
there are many indel hotspot discovery in the paper of "Accelerating discovery of functional mutant alleles in cancer" as below:
#================
We identified 1,165 statistically significant hotspot mutations of which 80% arose in 1 in 1,000 or fewer patients. Of 55 recurrent in-frame indels, we validated that novel AKT1 duplications induced pathway hyperactivation and conferred AKT inhibitor sensitivity.
#=================
but the hotspot soft will Discard the ins and del in soft script.
how can i get indel hotpsot in mydata？
thanks

SLC27A5:T554 location is out of range of Chr19 in the hotspot file

Hello,
Thank you very much for providing such a useful software. However, when I run my own data, the output result file has nothing but the column name. Empty results indicate that there are no hotspots or errors in operation.

Hi, could you please provide hotspot_algo.Rdata in hg38.

Thanks!