ANNOVAR Error: All variants in a VCF register as "invalid genotype records in input file"
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15 days ago

Hello, I am running into an error with convert2annovar.pl where it is registering all of the variants in my VCF as invalid. My VCF is 1925 variants plus the header with the following format:

CHROM POS ID REF ALT GENE QUAL FILTER FORMAT SAMPLE_INFO SAMPLE

chr1 69808 . G C OR4F5 361.47 PASS GT:AF 1/0:0.333 REDACTED

When I run perl convert2annovar.pl -includeinfo -allsample -withfreq -format vcf4 exome_calls_passvcf > exome_calls_pass.avinput

I receive the following output:

NOTICE: A total of 1925 locus in VCF file passed QC threshold, representing 1311 SNPs (752 transitions and 559 transversions) and 614 indels/substitutions
NOTICE: Finished writing allele frequencies based on 1311 SNP genotypes (752 transitions and 559 transversions) and 614 indels/substitutions for 2 samples
WARNING: 1925 invalid genotype records in input file

I have tried googling around, but I can't find other's getting this error. Has anyone run into it before? Thanks for the help!

genomics wgs vcf annovar • 346 views
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Hello, the problem is the file is not in VCF format. VCF format file should have header

#CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO, [FORMAT, ]

Where did you get the file?

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I got the file from another person who left the lab and am trying to validate their work. I tried restructuring the file to the VCF format you suggested but I am still getting the same error.

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I am sorry, I misunderstood you, you were trying to convert another format to VCF format. Maybe annovar document could help you.

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