Problem in converting vcf to maf using vcf2maf tools

Question

[Raheleh]

Hi,

I want to convert my vcf file (VarScan output) to maf file to generate some publication-quality images using maftools (R package). Based on the instruction of vcf2maf tools here, I installed VEP. But when I ran this command:

perl vcf2maf.pl --ref-fasta /home/raheleh/.vep/homo_sapiens/86_GRCh38/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz --input-vcf HROC.vcf --output-maf tests/test_varscan.vep.maf --tumor-id WD1309 --normal-id NB1308 --vcf-tumor-id TUMOR --vcf-normal-id NORMAL

I get this error:

ERROR: Provided --filter-vcf is missing or empty: /home/raheleh/.vep/ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz

Then I ran this command:

curl -L ftp://ftp.broadinstitute.org:/pub/ExAC_release/release0.3.1/subsets/ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz > $VEP_DATA/ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz

But I got this:

bash: /ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz: Permission denied

Can anyone help me how to fix it? Thank you!

[h.mon]

For the second error, it seems the variable $VEP_DATA is empty or non-defined, so you are trying to write a file to the root of the filesystem, which you, as a regular user, doesn't have permission to do. Define it with:

export VEP_DATA=/path/to/vep/data

[Raheleh]

@h.mon Thank you. I defined it with export VEP_DATA=/path/to/vep/data but now the error changed to this:

bash: /path/to/vep/data/ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz: No such file or directory

can you please help me?

[h.mon]

You have to use the actual path to VEP data - the one you used when installing VEP - not "/path/to/vep/data/".

[Kevin Blighe]

What h.mon means is that, if you have VEP installed at /Raheleh/programs/vep/, then you should use, for example:

export VEP_DATA=/Raheleh/programs/vep/data/

So, where have you installed VEP?

[Raheleh]

Oh, yeah. I did exactly as it is said here , so I think the path must be this export VEP_DATA=$HOME/.vep, right?

when I open terminal in the folder that I installed VEP, it shows this path: ~/vep

[Raheleh]

Is there any other ways to convert vcf to maf?

[Kevin Blighe]

I honestly would not bother to use MAF - the format never became popular. If you have a VCF, use bcftools query to nicely output the data that you then later want to use in R.

[Raheleh]

@Kevin Blighe I ran this command

bcftools cnv -c normal_rmdup.bam -s tumor_rmdup.bam -o outdir/ -p 0 Somatic.hc.fpfilterPassed.vcf

to produce a plot of my CNV file but I got this error: The sample "tumor_rmdup.bam" not found

The sample exist in the same directory as others. What's the problem? please help me out. Thank you!

Could you please also provide me with the command that you used to get a good output to be used in R? which R package can be used to visualize VCFs and CNVs? I really appreciate any help.

[Kevin Blighe]

I have not used bcftools cnv, however, I believe -s parameter is looking for a sample name from within your VCF file.