How to Specify Genome Build in MutSigCV Input ?

Question

[H.Hasani]

Hello,

I wonder if there is a way to to specify the genome assembly given to MutSigCV? I would like to use GRCh37.75 as I'm getting the following error :

Error using MutSigCV>MutSig_preprocess (line 542)
probable build mismatch between mutation_file and chr_files

For I've been using the reference files coming with the tool.

I'm very grateful for any quick help

[ssekar]

Hi,

Were you able to resolve this issue? I am running into the same problem now.

Thanks!

[H.Hasani]

Unfortunately no! I would love to know how!

Answer 1

[jz314]

I had this issue as well using the reference files that came with the tool, and it turned out I had a 1-off error- on the Start_position in the input mutation file. It should be 1-based relative to the Reference_Allele.
The way I figured this out was to check the base at specific positions in the provided reference files with commands such as head -c <position> chr1.txt|tail -c 1 and make sure the output matched the Reference_Allele base(s) in my input maf.
If you wanted to use a custom genome build instead of the hg19 provided, your format would probably need to be similar to the provided files, 1 file per chromosome with no linebreaks, so you'd have to convert a typical fasta accordingly (something like cat <your_reference_fasta_chromosome>|grep -v ">"|awk '{printf $1}' > <out_chr.txt>