search

UMCUGenetics / MutationalPatterns

R package for extracting and visualizing mutational patterns in base substitution catalogues
MIT License
104 stars 45 forks source link

Alternative input formats #42

Closed yunguan-wang closed 5 years ago

yunguan-wang commented 5 years ago

Hi ,firstly, thanks for the nice tool. I have some processed mutation information in a customized format. I tried to add relevant information such as #CHROM, POS, REF, ALT and constructed a 'fake' vcf files with header and mutation info. But I was not able to load these vcf with read_vcf_as_grange function. Can you tell me what is the required vcf columns needed for your program? Thanks! Yunguan

roelj commented 5 years ago

Hi @yunguan-wang, You need at least the required fields (CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO, FORMAT), and a GT format field.

Also, make sure that your self-created VCF files are valid according to the specifcation.