Entering edit mode
6.7 years ago
GK1610
▴
120
Hi I have 2 vcf files vcf1 from WGS data vcf2 from genotype data I am trying to merge these two files using combinevariants
GenomeAnalysisTK_jar=gatk/3.5-0/GenomeAnalysisTK.jar
java -jar $GenomeAnalysisTK_jar -T CombineVariants -R $REF --variant $vcf1 --variant $vcf2 -o $outputfile
I am getting this error
MESSAGE: The provided variant file(s) have inconsistent references for the same position(s) at 21:11098723, T* vs. A*
ERROR ------------------------------------------------------------------------------------------
when i grep these position in vcf1
21 11098723 . T C
21 11098724 . G A
vcf2
21 11098723 exm1562347 A G
how can i fix this error?
you cannot have two differents alleles at the same position at 11098723. It looks more like a bug in your upstream worklow (working with two different builds ?).
grep out the bad lines, or replace the reference allele ?
You could try updating all REF alleles t match a particular reference genome by using
bcftools norm
with the following command-line parameters:...although it rarely appears to function.
Thanks, yeah this works :)