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VariantAnnotator Annotation Error
I'm trying to annotate using VariantAnnotator, when I run:
java -jar GenomeAnalysisTK.jar -T VariantAnnotator -R ucsc.hg19.fasta --variant LK8851-Clean.vcf --resource LK8851-Clean-snpEff.vcf -L LK8851-Clean.vcf -o LK8851-Clean-VA.vcf
I get the following error:
Your input file has a malformed header: The FORMAT field was provided but there is no genotype/sample data
One of the variant lines:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT
1 14907 rs79585140 A G 661.53 MQFilter40 . .
I downloaded the vcf from https://my.pgp-hms.org/ and had to add the "." in the INFO and FORMAT columns because I was getting the error:
Line 128: there aren't enough columns for line 1 14930 rs75454623 AG 1103.37 MQFilter40 . (we expected 9 tokens, and saw 8 )
I'm new to this, I really searched a lot, but couldn't find anything useful, probably a very stupid error, but I would really appreciate your help.
Thank you for your time,