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