'a malformed header' error message with known indel vcf

shbriefshbrief New YorkMember
edited November 2016 in Ask the GATK team

Hi!
One of the Indel reference vcf files, which I'm trying to use for '-known' argument during RealignerTargetCreator step, gives me an error and I'm not sure how to solve this problem. (I've searched a bunch of references and not been successful...)

Here is the Indel reference vcf file giving me an error:
ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf
(ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/GRCh38_reference_genome/other_mapping_resources/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz)

Here is the error message I'm getting now:

ERROR MESSAGE: Your input file has a malformed header: Unexpected tag POS in line <ID=POS=POS-1,Number=0,Type=Flag,Description="POS has been adjusted due to missing REF in NCBI VCF file">

Any comment is welcomed. :)
Thank you for your time!

  • Sehyun

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