Problem with .vcf annovar

Question

[zizigolu]

Hi,

I faced a problem

I am trying to annotate my .vcf files by annovar to get maf as by maf I am able to visualize and do many things. I tried both vcf 4.1 and 4.2

[fi1d18@cyan01 annovar]$ table_annovar.pl my.vcf humandb/ -buildver hg19 -out myanno -remove -protocol refGene,cytoBand,exac03,avsnp147,dbnsfp30a -operation gx,r,f,f,f -nastring . -csvout -polish -xref example/gene_xref.txt

Annovar returns empty annotation

I tried to convert my vcf in annovar but I got

[fi1d18@cyan01 annovar]$ convert2annovar.pl -format vcf4 /tmy.vcf  > ex2.avinput                                 WARNING to old ANNOVAR users: this program no longer does line-to-line conversion for multi-sample VCF files. If you want to include all variants in output, use '-format vcf4old' or use '-format vcf4 -allsample -withfreq' instead.
Error: invalid record in VCF file: the GT specifier is not present in the FORMAT string: <1       10445   .       A       G       .       LowEVS  SOMATIC;QSS=1;TQSS=1;NT=ref;QSS_NT=1;TQSS_NT=1;SGT=AA->AA;DP=562;MQ=23.95;MQ0=232;ReadPosRankSum=0.46;SNVSB=0.00;SomaticEVS=0.10    DP:FDP:SDP:SUBDP:AU:CU:GU:TU    69:29:1:0:38,261:2,14:0,4:0,4     38:16:0:0:20,168:0,7:2,7:0,1>

I tried online annovar says I got the same error

I really need a maf file from my .vcf files

I don't know what is the solution? Converting vcf 4.1 to 4 compatible with annovar?

Any help please?

Answer 1

[zizigolu]

I found that convert2annovar.pl is okay with converting .vcf files coming from Mutect, VarScan, Delly even vcf 4.1 but not vcf 4.1 coming from Strelka. So because my variant caller was Strelka I was getting error. May be the easiest way for getting maf rom .vcf is vcf2maf but for that I needed to locate my data in VEP, I was not able to bind my data to the path to where VEP had been installed so I had to use Annovar for getting maf.

Answer 2

[onemoreuser]

Did you try Ensembl VEP online? It´s easy to use and you get MAF as output by default.

[zizigolu]

I don't need VEP itself rather I needed getting maf file for getting mutational visualization but vcf2maf tool needs VEP, I had installed VEP but I was getting this error says fasta file missing from vep