I am trying to extract snps out of merged vcf file using gatk SelectVariants command but it is giving following error:
htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately **line number 73**: Duplicate allele added to VariantContext: G, for input source: merged.vcf
This is line 7 of vcf file:
Kindly provide your valuable suggestions to resolve this error.
Many thanks
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written
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Bushra Bibi
This is an error in your input vcf file. The REF allele MUST be different from the ALT allele.
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Pierre Lindenbaum
Yes Pierre there is lower case g in REF and upper case G in ALT field. My question is that why variant caller is calling opposite case allele as variant when its not and how can I overcome it? I used callvariants.sh for variant calling.
Thanks
Not only opposite case but same case nucleotides are also present in vcf fle.
again, it's a problem with the variant caller, which is ?
Its bbmap tool callvariants.sh. I think you are right because I did not get such error when I called variants through freebayes.
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I observed that my reference genomic fasta file contains both lower case and upper case nucleotides. Do I need to convert lower case nucleotides into upper (all nucleotides in one case) before calling variants? I performed variant calling through bbtool callvariants.sh.