#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT tumor|normal
chr1 1789227 . C T 104 Q10;SN1.5;NM5.25;AMPBIAS SAMPLE=tumor|normal;TYPE=2;0;DP=1443;END=1789227;VD=5;AF=0.0035;BIAS=2:2;REFBIAS=647:791;VARBIAS=3:2;PMEAN=36.4;PSTD=1;QUAL=45;QSTD=0;SBF=60;ODDRATIO=10;MQ=0.0035;SN=0;HIAF=1.4;ADJAF=0.6627;SHIFT3=0.54554;MSI=2012;MSILEN=0;NM=948;HICNT=1064;HICOV=0;LSEQ=0;RSEQ=C/C;GDAMP=36.2;TLAMP=1;NCAMP=44.9;AMPFLAG=1 GT:DP:VD:AD:AF:RD:ALD 0/1:1443:5:1438,5:0.0035:647,791:3,2
I think TYPE=2;0 might be a formatting issue. When I try to run picard's sortvcf on this vcf file, I get this error:
Exception in thread "main" java.lang.IllegalStateException: Key 0 found in VariantContext field INFO at chr1:1789227 but this key isn't defined in the VCFHeader. We require all VCFs to have complete VCF headers by default.
It is complaining because it thinks 0 is an undefined key since a semicolon is used as a delimiter in TYPE=2;0.
Dear Vardict developers,
Here is the first variant identified by Vardict:
I think
TYPE=2;0
might be a formatting issue. When I try to run picard's sortvcf on this vcf file, I get this error:It is complaining because it thinks
0
is an undefined key since a semicolon is used as a delimiter inTYPE=2;0
.Here is my code:
I would appreciate any insights!