Question: Error : Duplicate allele added to VariantContext GATK
0
gravatar for steven.blanchard92
6 months ago by
steven.blanchard920 wrote:

Hello,

I download GnomAD vcf files in GRCh38 (hg19 remap). I want to convert this vcf in a table so i try to use VariantsToTable. But i have this error : The provided VCF file is malformed at approximately line number 10609: Duplicate allele added to VariantContext: C

line 10609 :

10 3101451 rs4881080 C C,T,G 191085017.71 PASS AC=237624,66,1;AF=9.99663e-01,2.77656e-04,4.20691e-06

I agree C is in REF and ALT colum but we can use VariantsToTable without check the integrity of vcf files?

Thanks,

Steven

ADD COMMENTlink modified 6 months ago by Pierre Lindenbaum112k • written 6 months ago by steven.blanchard920
0
gravatar for Pierre Lindenbaum
6 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum112k wrote:

can use VariantsToTable without check the integrity of vcf files?

not GATK uses the htsjdk library and there is no 'boolean flag' to bypass the validation:

https://github.com/samtools/htsjdk/blob/master/src/main/java/htsjdk/variant/variantcontext/VariantContext.java#L1490

if it's not a problem for your analysis, you could use awk to replace all the REF bases to 'N' (?)

ADD COMMENTlink written 6 months ago by Pierre Lindenbaum112k

Thank you, but I can not change all REF to N. I need REF to annotate deletions

ADD REPLYlink written 6 months ago by steven.blanchard920

I am getting the error as ERROR MESSAGE: The provided VCF file is malformed at approximately line number 271180: Duplicate allele added to VariantContext: AATTTATATATATATATATATATATATATATATATATATATATATATATATATATATATATAAATT" GATK combine variant. Is it ok to delete the perticulat line from vcf file. I have obtained vcf file from samtools.

ADD REPLYlink written 6 months ago by vivekruhela10
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