[Vcftools-help] (no subject)

[Dami G. <dam...@ya...>]

Sorry - had sent this to the wrong list, so am resending.

I am running vcf-consensus, but there is an error as

"The fasta sequence does not match the REF at NC_002516.2:1461409. GCA(CAGCCGCC) in .fa, TCG in .vcf"

Don't know why this is happening, I am using the same reference file. The error is thrown in the code at

 # Sanity check

 if ( substr($$vline[3],0,$ref_len) ne substr($$opts{fa_buf},$pos,$ref_len) ) 
 { 
       error(sprintf "The fasta sequence does not match the REF at $$vline[0]:$$vline[1]. %s(%s) in .fa, %s in .vcf\n",     substr($$opts{fa_buf},$pos,$ref_len),substr($$opts{fa_buf},$pos+1,$ref_len+5),substr($$vline[3],0,$ref_len));
 }

So I have commented this out, don't know if this is the best thing to do. Any ideas?
Thanks very much.