Hi
Has any one tried using GATK with a non-model organism? If so kindly, would you tell me the format of the VCF files you are using? I was reading few posts at the GATK forum and got details about makings a VCF file. Below is a snap shot of mine VCF file.
##fileformat=VCFv4.0
#CHROM POS ID REF ALT QUAL FILTER INFO
1 11613 . C A . PASS .
1 12971 . T G . PASS .
1 13003 . T A . PASS .
1 13032 . A G . PASS .
GATK does make the tribble index file but at the end throws an error saying that "The provided VCF file is malformed at approximately line number 56981: The VCF specification does not allow for whitespace in the INFO"
The INFO column has ".", which i found was used by other for making a VCF file. Do i have to use VCF validate it? I do know VCF tools but think this file will not be able to pass it.
I would appreciate any help as i am stuck and need to complete this....
Thanks
Has any one tried using GATK with a non-model organism? If so kindly, would you tell me the format of the VCF files you are using? I was reading few posts at the GATK forum and got details about makings a VCF file. Below is a snap shot of mine VCF file.
##fileformat=VCFv4.0
#CHROM POS ID REF ALT QUAL FILTER INFO
1 11613 . C A . PASS .
1 12971 . T G . PASS .
1 13003 . T A . PASS .
1 13032 . A G . PASS .
GATK does make the tribble index file but at the end throws an error saying that "The provided VCF file is malformed at approximately line number 56981: The VCF specification does not allow for whitespace in the INFO"
The INFO column has ".", which i found was used by other for making a VCF file. Do i have to use VCF validate it? I do know VCF tools but think this file will not be able to pass it.
I would appreciate any help as i am stuck and need to complete this....
Thanks
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