VariantFiltration weird error

[francois.sabot]

Hi everyone
It was a long time since I do not have a bug...

I was trying to filter my raw vcf data (both SNP and InDel in the same file, all sites emited), from rice (plant...), and I use this command in variation filter:

java -jar /home/***/sources/GenomeAnalysisTK/GenomeAnalysisTK.jar -T VariantFiltration -R /home/***/Documents/reference/***.fasta --variant all_cleaned_raw.vcf -o all_cleaned_filtered.vcf --clusterWindowSize 0 --filterExpression "MQ0 >= 4 && ( (MQ0 / (1.0 * DP)) > 0.1)" --filterName "HARD_TO_VALIDATE" --genotypeFilterExpression "DP < 10" --genotypeFilterName "UNSURE"

It works well until this comment and error...

##### ERROR MESSAGE: Badly formed variant context at location chr01-13101:1192; no padded reference base was provided.

And the corresponding line is

chr01-13101 1192 . G . 87.15 PASS AC=0;AF=0.00;AN=8;DP=119;MQ=51.72;MQ0=0 GTP:GQ:PL 0/0:17:51.15:0,51,624 0/0:36:99:0,108,1443 0/0:39:99:0,117,1595 0/0:27:81.23:0,81,1003

I cannot figure out the error. Can someone help me ?

Cheers

Francois