Rea Kalampaliki
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hs37d5 genome in the GATK bundle
AnsweredFollowing a previous post: BaseRecalibrator - no suitable codecs – GATK (broadinstitute.org) I think that my problem lies on not choosing correctly the reference genome for my samples. I was given ...
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Difference in contigs between hg19_v0_Homo_sapiens_assembly19.fasta and hg19_v0_1000G_omni2.5.b37.vcf.gz and Mills_and_1000G_gold_standard.indels.hg19.sites.vcf files?
Answereda) GATK version used: v4.2.5b) Exact command used: BaseRecalibrator I am receiving an error for incompatible contigs. I think both files use for known variants, hg19_v0_1000G_omni2.5.b37.vcf.gz and...