Hi I have snps from rnaseq data. I split multisample file into single sample files. Now each sample vcf, I want to convert vcf to maf in vcf2maf . I am getting following error
perl /usr/local/bin/vcf2maf.pl --input-vcf F545_altref_vep.vcf --output-maf F545_altref_vep.maf --tumor-id WD1309 --ref-fasta Homo_sapiens.GRCh38.dna.toplevel.fa.gz
>ERROR: Your VCF uses CR line breaks, which we can't support. Please use LF or CRLF.
I will appreciate all the suggestions
Thank you Archana
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Omics data mining
Why not just using sed? :)
sed 's/\r/\n/' F545_altref_vep.vcf > F545_altref_vep_fixed.vcf
I was running vcf2maf on Linux and came across the same problem. So, my question is: are you running it on Linux as well?
If so, it seems that this is a matter of line break system in different OS.
Fortunately, that can be easily fixed by dos2unix command.
In my case, I ran:
dos2unix -n -ascii Old.vcf New.vcf
Where, -n will generate a new file whilst keeping the original; and -ascii will convert only the break lines.
I hope it helps.
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Did you edit the file somewhere? Where? It is complaining about the file having lines delimited by carriage return, which was used on old Macs. This is the comment on the code:
With what software did you split the multi-sample file into single files? It looks like that software introduced something the perl script doesn't like.