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Error: htsjdk.tribble.TribbleExpection: The provided VCF file is malformed at approximately line number 5880: Duplicate allele added to VariantContext: GT

I am trying to index a vcf file using igvtools. For some reason, I am getting the following error. 

Error: htsjdk.tribble.TribbleExpection: The provided VCF file is malformed at approximately line number 5880: Duplicate allele added to VariantContext: GT

When I got to the specific line it looks like the vcf has the reference duplicated in the alteration column. Here is what it looks like 

1   19723050    rs9004957   GT  G,GT    .   .   RSPOS=19617712;RV;dbSNPBuildID=118;SAO=0;VC=in-del;VLD;VP=050000000005000100000200

When I go into the vcf and fix the line by removing the extra GT in this case, then I get another error about the same issue but just thousands of lines later in the VCF. If this happened just a couple of times I would just manually fix them but there are too many occurrences to do that in this case. I was wondering if there was a way to fix this?

snp genome next-gen assembly
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updated by aldhairmedico • aldhairmedico • written by williamsbrian5064 williamsbrian5064

3 answers 

awk -F '\t' '/^#/ {print;next;} {OFS="\t";R=$4;n=split($5,a,/[,]/);s="";for(i=1;i<=n;i++) {s=sprintf("%s%s%s%s",s,(i==1?"":","),a[i],a[i]==R?"AAAAAAAAA":"");} $5=s; print;}' < input.vcf
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written by Pierre Lindenbaum Pierre Lindenbaum

That worked like a charm. I change it a bit to create a new file. Here is what I did for anyone else that encounters this error

awk -F '\t' '/^#/ {print;next;} {OFS="\t";R=$4;n=split($5,a,/[,]/);s="";for(i=1;i<=n;i++) {s=sprintf("%s%s%s%s",s,(i==1?"":","),a[i],a[i]==R?"AAAAAAAAA":"");} $5=s; print;}' old.vcf > new.vcf
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written by williamsbrian5064 williamsbrian5064

change is you just added old.vcf > new.vcf to the code

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written by DareDevil DareDevil

It's easier to use vcftools.

vcftools --remove-indels --recode --recode-INFO-all --vcf old.vcf --stdout >new.snp.vcf

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written by Sam • Sam

I had a similar problem using GATK BaseRecalibrator and Ensembl v103 VCF files for --known-sites. I initially thought that it was a version problem but even using the latest version for GRCh38.p13 (v109) I still had the same issue.

Errors: A USER ERROR has occurred: Error while trying to create index for homo_sapiens-chr3.vcf. Error was: htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 4431575: Symbolic alleles not allowed as reference allele: <W>

A USER ERROR has occurred: Error while trying to create index for homo_sapiens-chr17.vcf. Error was: htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 19739670: Symbolic alleles not allowed as reference allele: <Y>

So I just got rid of all symbolic refs, characterized by having <>. However if you are dealing with CNVs or Structural variants this is not recommended:

input_vcf="homo_sapiens-chr17.vcf"
output_vcf="homo_sapiens-chr17_wo_symbolic_refs.vcf"

awk 'BEGIN {FS=OFS="\t"} /^#/ {print; next} $4 !~ /[<>]/ {print}' $input_vcf > $output_vcf

Apparently, GATK expects a single allele in the reference. After this change, it worked. P.S. for some reason only chr3 and chr17 had this problem.

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written by aldhairmedico • aldhairmedico

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