Providing input file for software

[MaryGoAround]

Sorry

Is there any function in your software which extracts require fields like CHR, POST, REF, ALT, VAF, ... from a .vcf file (SNP or INDEL or SV) ?

Because extracting these fields seems to be a bit time consuming

I have tried this function

DBS_input <- palimpsest_input(vcf="sample.vcf", Type = "DBS")
Error in palimpsest_input(vcf = "sample.vcf",  : 
  vcf is missing the DBS mutation category column. Use the << annotate_VCF >> function to add the appropriate column.
> 
> 

Thank you for any information

[benedict909]

Hi,

Sorry there is no specific function for this in the package.

If you have a file like the example here, you should just be able to remove the header in a text editor and use it in Palimpsest.

However, the error you're seeing here could be caused by not having used the annotate_VCF function to add the "DBS_cat" column, which must be done before using the palimpsest_input function.

I hope this helps!
Benedict

[N-TI]

Hi,
I have a vcf file like the example in wikipedia and i can not use in Palimpsest even when I removed the header. I had this error

Error in load(file.path(datadir, "file.vcf")) :
bad restore file magic number (file may be corrupted) -- no data loaded
In addition: Warning message:
file ‘file.vcf’ has magic number 'CHROM'
Use of save versions prior to 2 is deprecated

Thank u