Question: A small detail when use VEP
0
gravatar for Laven9
11 months ago by
Laven90
Laven90 wrote:

It is a small question I met when running vcf2maf (VEP): If you run vcf2maf (VEP), there is a fasta file needed to be offered. And my question is: since I used hg38.fa for my previous work, which fasta file should I give? hg38.fa or Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz from VEP? As researched, I got the notion that the difference between hg38 and GRCh38 is only the contigs like chrx VS x, so I suppose it doesn't matter and I could choose either of the two. Am I right?

vep • 230 views
ADD COMMENTlink modified 11 months ago by WouterDeCoster44k • written 11 months ago by Laven90
1
gravatar for WouterDeCoster
11 months ago by
Belgium
WouterDeCoster44k wrote:

the difference between hg38 and GRCh38 is only the contigs like chrx VS x, so I suppose it doesn't matter and I could choose either of the two

I don't know for this tool (vcf2maf) specifically, but it definitely does matter for most tools. Always use the same reference for one project. If you used hg38.fa for alignment, then stick to it.

ADD COMMENTlink written 11 months ago by WouterDeCoster44k

I see your point! Thank you for your advice!

ADD REPLYlink written 11 months ago by Laven90
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