Haplotype database for finger print

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Heba B abusamra

• September 10, 2020 09:03

If you are seeing an error, please provide(REQUIRED) :
a) GATK version used:
b) Exact command used:
c) Entire error log:

If not an error, choose a category for your question(REQUIRED):
a)How do I (......)?
b) What does (......) mean?
c) Why do I see (......)?
d) Where do I find (......)?
e) Will (......) be in future releases?

java -jar picard.jar CheckFingerprint \
          INPUT=sample.bam \
          GENOTYPES=sample_genotypes.vcf \
          HAPLOTYPE_DATABASE=fingerprinting_haplotype_database.txt \
          OUTPUT=sample_fingerprinting 

Where I can get/download  the haplotype database file ?

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• 

  Genevieve Brandt (she/her)

  • September 10, 2020 22:15

  Please see the documentation for the most recent explanation of this tool and how to run it: https://gatk.broadinstitute.org/hc/en-us/articles/360047216131-CheckFingerprint-Picard-

  More information on haplotype map format: https://gatk.broadinstitute.org/hc/en-us/articles/360035531672-Haplotype-map-format

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  Heba B abusamra

  • September 13, 2020 05:34

  Thanks for your help

  I already read the link, however the link https://software.broadinstitute.org/gatk/documentation/article?id=9526 

  is not working

  --HAPLOTYPE_MAP  -H

  The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for fingerprinting. See https://software.broadinstitute.org/gatk/documentation/article?id=9526 for details.

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  Genevieve Brandt (she/her)

  • September 14, 2020 20:45

  Hello Heba B abusamra, I believe the file that should be linked there is this one (https://gatk.broadinstitute.org/hc/en-us/articles/360035531672-Haplotype-map-format).

  We are still in the process of updating the links from our old website to go to our new articles. Sorry for the confusion!

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