Question: How to get TCGA SNP in vcf and process in PLINK
0
gravatar for archie
22 months ago by
archie90
India
archie90 wrote:

Dear all

I urgently want to download SNP information of TCGA-PAAD and run in PLINK for further analysis . I got the expression data of 183 samples. Is It possible to get SNPs of 183 samples in VCF ?

waiting for reply

All suggestions will be appreciated

Thank you in advance

Archana

plink tcga vcf • 508 views
ADD COMMENTlink modified 22 months ago by pbpanigrahi190 • written 22 months ago by archie90
0
gravatar for pbpanigrahi
22 months ago by
pbpanigrahi190
pbpanigrahi190 wrote:

Download the snp information as maf format, then you can convert maf to vcf format using https://github.com/mskcc/vcf2maf/blob/master/maf2vcf.pl

ADD COMMENTlink modified 22 months ago • written 22 months ago by pbpanigrahi190

Hi

I did the same. During runtime of maf2vcf.pl I am getting warning

WARNING: Reference allele mismatches found.

Many of SNPs are getting filtered out . What should I do ?

ADD REPLYlink written 22 months ago by archie90

I checked respective position on given genome build, It was exactly same. Still I am getting this issue. Can anybody suggest me how to fix it ? Otherwise I will lose most of the SNPs information for downstream which I do not want to do. Or If its possible to create manual vcf ? How ?

ADD REPLYlink modified 22 months ago • written 22 months ago by archie90

Can u post the command u typed. Also are u getting many vcf files in the output folders? Because the code generates a vcf file per tumor-normal sample pair. Are u getting only the specific error u mentioned earlier, or other error. Detailed information will help us to debug. Else provide the input file.

ADD REPLYlink written 22 months ago by pbpanigrahi190

Hi

First of all, defined the ref fasta my $ref_fasta = "/path/Homo_sapiens.GRCh37.75.dna.toplevel.fa" in script maf2vcf.pl and saved changes. Here is command used to convert maf to vcf .

perl maf2vcf.pl --input-maf TCGA-IB-8127-01.maf.txt --output-dir TCGA-IB-8127-01.vcf

Thank you in advance Archana

ADD REPLYlink modified 22 months ago • written 22 months ago by archie90
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1240 users visited in the last hour