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Hi Geraldine, yes I figured it out. I was initially accessing ftp://ftp.broadinstitute.org/bundle/ through Internet Explorer and for some reason it wasn't loading the updated version 2.5. But when I accessed the resource bundle through wget ftp://gs…
Hello, I haven't had any luck in locating the 1000 Genomes Phase 1 SNPs VCF in the resource bundle at ftp://ftp.broadinstitute.org/bundle/2.3/. I only see the 1000G Phase 1 indels file. Which resource file can I use for the VariantRecalibrator step?
Hello, I have a few questions that I would like to clarify: * Is the file 1000G_phase1.snps.high_confidence.vcf available in the resource bundle? (I looked it up and it wasn't there!) If not, which file is recommended with the updated VariantRecali…
Yes I restricted my calls to intervals in a bed file. I ran HaplotypeCaller without interval padding but I modified the bed file such that it is padded by 50 bp with the overlaps merged. The total length of the intervals in my modified bed file is a…