snpEff error

[sinnamone]

Hi,
I'm using snpEff and when i type:
java -Xmx2g -jar snpEff.jar -o vcf Helicobacter_pylori_26695_uid57787 xxx.vcf > xxx_ou.vcf

I get this :

ERRORS: Some errors were detected
Error type Number of errors
ERROR_CHROMOSOME_NOT_FOUND 65454

[smars0001]

You need to look at the CHROM field in the vcf file and compare the identifiers used in the snpEff db... take a look at the std out from the snpEff.. it should point you to the problem (i.e identifier mismatch)

[sytiger]

I got the same error. I did check the chromosome name in the vcd file and the database bin file. They are the same.

I am testing the SNP of Staph aureus

[am@i]

Hello everyone,
I want to compare snpeff result between two samples. ANy recommendations for softwares for this? I obviously will compare SNP and INDELS etc?

Thank You in advance