Test-drive the GATK tools and Best Practices pipelines on Terra
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about the resource bundle for hg38 : about the vcf files
Dear all, please could you let me know whether there is a quick fix for the VCF files in the bundle for hg38
(available at ftp://ftp.broadinstitute.org/bundle/hg38/hg38bundle/): particularly,
- dbsnp_144.hg38.vcf has the chromosomes names as "1,2, ..." etc instead of "chr1, chr2, " etc
- dbsnp_138.hg38.vcf is missing (I can see only "dbsnp_138.hg38.vcf.gz.tbi" file).
and also I would appreciate some information on the following:
what is the difference between 1) "Homo_sapiens_assembly38.dbsnp.vcf" and 2) "Homo_sapiens_assembly38.dbsnp138.vcf" ?
which one of these files above 1) or 2) shall I use for base score recalibration ?
what is the difference between the files 3) "Homo_sapiens_assembly38.known_indels.vcf" and 4) "Homo_sapiens_assembly38.variantEvalGoldStandard.vcf", and when shall I use those in the analysis ?