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Most columns are empty within MAF #203
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Dear @weichisyu, Thanks for your interest in PCGR, I am happy you find it useful:-) I will go through the MAF generation to see how we can populate the MAF with more data. You essentially want more of the data provided from PCGR annotation in your MAF, right? best, |
Dear @sigven For now, the input for vcf2maf within PCGR is unannotated vcf and using But, it sounds great if the MAF could have more of the data provided by PCGR annotation. (It means adding more columns right?) best, |
Dear Weichi, I think your suggestion regarding feeding vcf2maf with the VEP-annotated VCF might be the best solution, I will try to set this up. best, |
Hi Sigven,
Thanks for this wonderful project.
Recently I use PCGR to get both HTML report and MAF.
It seems that the file input to vcf2maf isn't annotated, so most column are empty in the final MAF.
I found that it could get the MAF with annotated information by put either
.pcgr_ready.vep.vcf
or.pcgr_acmg.grch38.vcf
which already annotated by PCGR into vcf2maf.Is it possible to have a true/false argunment let user make PCGR put those annotated vcf into vcf2maf? Or passing the annotated vcf into vcf2maf directly within PCGR?
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