vcf2maf
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mskcc
Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
I follow the readme n varscan but I have some problems on the VF calclucation on tvaf. Inside the value the report the percent...how can caluclate the VAF correcly on...
The following gist: https://gist.github.com/ckandoth/f265ea7c59a880e28b1e533a6e935697 seems to only work for linux systems. Is there an equivalent one for Mac OS? Also, does vcf2maf only work for VEP v86, but not newer...
It's not listed at https://useast.ensembl.org/info/genome/variation/predicted_data.html#consequences but it still shows up in the results of a large project. vcf2maf assigns it the lowest priority by default.
The [current gist](https://gist.github.com/ckandoth/f265ea7c59a880e28b1e533a6e935697) to download the ExAC VCF and whitelist known somatic events, will also inadvertently whitelist indels that overlap these known somatic events. Fixing this will take some work....
This bug has always existed. It happens because `maf2maf` uses `maf2vcf` to create a deduplicated multi-sample VCF for VEP, and `FILTER` tags are necessarily merged across samples. The solution might...
It would be nice to be able to use RefSeq or Merged caches (VEP options `--refseq` and `--merged`), instead of being forced into just using the Ensembl cache. So far...
Hi， This is my sample vcf file: chrM 593 . T C . PASS AS_FilterStatus=SITE;AS_SB_TABLE=1,0|172,137;DP=317;ECNT=3;MBQ=30,25;MFRL=220,155;MMQ=60,60;MPOS=27;OCM=0;POPAF=2.40;TLOD=883.55 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:1,309:0.992:310:1,85:0,91:1,247:1,0,172,137 chrM 625 . G A . PASS AS_FilterStatus=SITE;AS_SB_TABLE=225,176|2,2;DP=420;ECNT=3;MBQ=18,20;MFRL=147,137;MMQ=60,60;MPOS=34;OCM=0;POPAF=2.40;TLOD=1.43 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:401,4:9.722e-03:405:7,0:6,1:311,2:225,176,2,2 chrM 750 ....
add the possibility to have filenames with special characters properly processed. Being a consortium with 20+ participating sites, we have input files naming that are out of control. Sometimes, the...
Hi there, I am reading a maf file, converted with vcf2maf.pl from https://github.com/mskcc/vcf2maf I converted it from a VCF which only have PASS variants like this: perl vcf2maf.pl --input-vcf /Users/abelgd/Desktop/training_bioinfo/VCFs_pipeline_curro/tejidos_vcfs_PASS/descomp/PCT75.filtered.PASS.vcf...
