Palimpsest
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Providing input file for software
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.
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Thank you for any information
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
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