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VCF data can only be configured as a URL, not uploaded directly. Directions are found at http://genome.ucsc.edu/goldenPath/help/vcf.html.

• The VCF file must be sorted by chromosome and position (most tools produce VCFs like this).
• The VCF file must be compressed using bgzip:

  Code Block
  module load tabix # also loads bgzip cd $BI/web bgzip progeria_ctcf.vcf

• The VCF file must be indexed using tabix:

  Code Block
  tabix -p vcf progeria_ctcf.vcf.gz

This has already been done, and the resulting files are at this URL: http://loving.corral.tacc.utexas.edu/bioiteam/ucsc_custom_tracks/, filename progeria_ctcf.vcf.gz. These are hg18 SNP calls from published Iyer Lab CTCF ChIP-seq data in Progeria cells. The VCF file was produce using Broad's GATK.

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BAM data can only be configured as a URL, not uploaded directly. Directions are found at http://genome.ucsc.edu/goldenPath/help/bam.html.

• The BAM file must be sorted and indexed using samtools. The .bam and .bai index file must reside in the same directory.

This has already been done, and the resulting files are at this URL: http://loving.corral.tacc.utexas.edu/bioiteam/ucsc_custom_tracks/, filename hela_totrna.sorted.bam. This is SE RNAseq data mapped directly to the human genome, hg19.

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