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Where might I download an hapmap for experimenting with GATK

DennyDenny Gulfport, MSMember

Error messages beaucoup attend the use of VariantsToVCF tool in the following command line:
java -jar gatk.jar -T VariantsToVCF -R reference.fa -o output1.vcf --variant:RawHapMap input.hapmap

Having tried several sources for hapmap download, all of the files used throw error messages. Using
/home/denny/DNATools/RefSeq/genotypes_chr10_ASW_r28_nr.b36_fwd.txt renamed to input.hapmap, here is the latest example:

ERROR MESSAGE: Input files /home/denny/DNATools/RefSeq/input.hapmap and reference have incompatible contigs. Please see https://www.broadinstitute.org/gatk/guide/article?id=63for more information. Error details: No overlapping contigs found.
ERROR /home/denny/DNATools/RefSeq/input.hapmap contigs = [chr10]
ERROR reference contigs = [KU679421.1|, ref|NC_030339.1|, ref|NC_028010.1|, HQ283100.1|, ref|NC_005362.1|, ref|NC_008074.1|, ref|NC_012147.2|, ref|NC_011127.2|]
ERROR ------------------------------------------------------------------------------------------

Where might I source a valid hapmap to use to bootstrap myself up the steep learning curve of Bioinformatics using gatk?

Answers

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