Approximate line numbers and dbsnp 142 (grch37)

TechnicalVaultTechnicalVault Cambridge, UKMember ✭✭✭

I get the following errors when trying to use dbsnp 142 with GATK (these are from 8 diff runs):

##### ERROR MESSAGE: The provided VCF file is malformed at approximately line number 122998: Duplicate allele added to VariantContext: A, for input source: /lustre/scratch113/resources/variation/Homo_sapiens/grch37/dbsnp_142.vcf.gz
##### ERROR MESSAGE: The provided VCF file is malformed at approximately line number 123010: Duplicate allele added to VariantContext: A, for input source: /lustre/scratch113/resources/variation/Homo_sapiens/grch37/dbsnp_142.vcf.gz
##### ERROR MESSAGE: The provided VCF file is malformed at approximately line number 123019: Duplicate allele added to VariantContext: A, for input source: /lustre/scratch113/resources/variation/Homo_sapiens/grch37/dbsnp_142.vcf.gz
##### ERROR MESSAGE: The provided VCF file is malformed at approximately line number 123017: Duplicate allele added to VariantContext: A, for input source: /lustre/scratch113/resources/variation/Homo_sapiens/grch37/dbsnp_142.vcf.gz
##### ERROR MESSAGE: The provided VCF file is malformed at approximately line number 123003: Duplicate allele added to VariantContext: A, for input source: /lustre/scratch113/resources/variation/Homo_sapiens/grch37/dbsnp_142.vcf.gz
##### ERROR MESSAGE: The provided VCF file is malformed at approximately line number 123022: Duplicate allele added to VariantContext: A, for input source: /lustre/scratch113/resources/variation/Homo_sapiens/grch37/dbsnp_142.vcf.gz
##### ERROR MESSAGE: The provided VCF file is malformed at approximately line number 123006: Duplicate allele added to VariantContext: A, for input source: /lustre/scratch113/resources/variation/Homo_sapiens/grch37/dbsnp_142.vcf.gz
##### ERROR MESSAGE: The provided VCF file is malformed at approximately line number 123000: Duplicate allele added to VariantContext: A, for input source: /lustre/scratch113/resources/variation/Homo_sapiens/grch37/dbsnp_142.vcf.gz

Unfortunately given the approximate line number I can't seem to figure out which variant is causing the issue. Help?

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