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• Converting TCGA MAF files to VCF using reference assembly GRCh37 lite
  Hello I am trying to convert TCGA MAF file to VCF using maf2vcf.pl The MAF file with build GRCh...
• converting maf to vcf
  Hi, I am working on exome data from tcga. I downloaded it in .maf format and want to convert it ...
• annotating MAF files
  I've read quite a few posts on this forum on MAF files: https://www.biostars.org/p/69222/ and ht...
• TCGA SNP to plink
  Hello everyone I want to convert from TCGA SNP to PLINK. Can anyone suggest here 1. I download...
• TCGA maf to vcf file conversion
  Hello All, I want to convert TCGA MAF to VCF analysis with PLINK I worked on the conversion of M...
• TCGA VCF & MAF content
  I have downloaded all the VCF files for one cancer type from the TCGA. Upon annotation using Ann...
• Tool or Script to convert MAF file to VCF ?
  Hi, Does anybody know of any script/tool which could convert a MAF file to VCF ? https://wiki.n...
• GRCh37/hg19 human genome sequences from NCBI
  Hello all, How can I download one single file containing all chromosomes sequences of GRCh37/h...
• TCGA Birdseed vs MAF vs VCF
  Hello, I am working with RNA-seq data from TCGA and wanted to find SNVs for the datasets. The da...
• Converting Vcf File To Maf
  I have a vcf file generated by in-house variant calling pipeline, containing both coding and non-...
• Consolidated MAF file for all cancers in TCGA
  Hi I want a consolidated MAF file for all cancers from TCGA data. Is it correct to use the MAF ...
• Maf to VCF file convertion, offline_cache not downloading
  Hi All, I am trying to replicate ensembl_vep_88_with_offline_cache.md as mentioned in this line ...
• ncRNA gencode files
  In gencode how can I download ncRNA for GRCH37 ( (=comprehensive) gtf file I see GRCH38 are there...
• How to download dbSNP153 vcf files in hg19/GRCH37 version
  Hi All, I notice dbSNP152 has been updated to dbSNP153 when I search rs533316401 https://www.n...
• Broad Institute TCGA MAF procedure
  I am calling snv and indels on tumor/matched normal RNA-seq data from TCGA using Mutect2. I am c...
• Convert BED(UCSC) to VCF
  I am using liftOver to convert hg19-hg38. I made BED file from VCF to run liftOver. How can I con...
• Vcf To Maf (Mutation Annotation Format) Conversion ?
  Is there any standard tool out there that can convert a VCF file to Mutation Annotation Format (M...
• how to extract mutation from MAF file in python
  I just downloaded data from tcga and GDC . I have two files , one is anotation.txt and other is ....
• Is GRCh37 and hg19 are the same?
  I would like to visualise some of my bam files on IGV, the reference genome used to analyse was G...
• vcf to MAF to fasta
  Dear all, A strange idea has came to my mind recently. There is no direct way to convert vcf in...
• How to convert vcf to MAF ?
  I'm interested in converting vcf to MAF, I found 2 scripts 1) perl vcf to maf Its ask for a EX...
• Is it possible to generate a single maf file from multiple vcf files using vcf2maf ?
  Hi, I have 40 raw vcf files and I was able to convert all these 40 vcf files to 40 individual m...
• TCGA SNP data
  Dear all In one of my project, I have to use the SNPs from TCGA (PAAD) and convert them into pl...