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NGS Scripts

There are several versions of the pipelines.  Several are somewhat historical as they expect older fastq files generated by Illumina RTA 1.3-1.7.  While the newer ones are design to expect current (ie. anything generated in 2011) HiSeq data were the fastq files were created on RTA 1.8, which encodes the quality values in Sanger format as opposed to the previous Illumina format that needed to be converted to the Sanger fomat most applications expect as default.
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Temporary Upload: Parallel version designed to work for the TGen Saguaro2 HPC environment. Should be easy to port to other HPC environments particularly any that use PBS job submission control. Future upload will contain headers from all required files listed in parameters.ini and a serial MacOS version  23k v. 2 Jan 18, 2012, 2:56 PM Jonathan Keats
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Cosmic mutant export version 57 converted to VCF specification  265k v. 3 Feb 9, 2012, 8:38 AM Jonathan Keats
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  2k v. 2 Sep 25, 2011, 11:17 PM Jonathan Keats
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This script takes a single column, no header text file with HUGO gene names or Ensembl gene IDs, as an input and pull out for all .expr files in the run folder  2k v. 4 Aug 25, 2012, 8:40 AM Jonathan Keats
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  536k v. 4 Nov 26, 2011, 11:32 PM Jonathan Keats
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Ribosome location file for Picard RNAseq metrics compatible with 1000 genomes reference file (ie. Ensembl 55).  29k v. 3 Apr 23, 2012, 11:17 PM Jonathan Keats
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  30k v. 2 Sep 25, 2011, 11:24 PM Jonathan Keats
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This will read in a VCF or Keats pipeline file, creating a IGV batch script to take a picture of each position in the provided file.   5k v. 5 Aug 6, 2012, 7:20 PM Jonathan Keats
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This script will convert VCFs with SnpEff canonical annotations into single and merged tab-deliminated text files using SnpSift and vcfEffOnePerLine.pl included in the SnpEff/SnpSift version3.3 download package   5k v. 2 Aug 25, 2013, 4:10 PM Jonathan Keats
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This Package will convert flowcell exports from the Keats Lab Database into the proper format for the TGen Pipeline  5k v. 3 Jul 28, 2012, 2:51 PM Jonathan Keats
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  5k v. 2 Sep 25, 2011, 11:22 PM Jonathan Keats
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Serial Pipeline for newer datasets created with RTA1.8 which outputs Sanger format quality values   57k v. 3 Nov 26, 2011, 11:32 PM Jonathan Keats
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  57k v. 3 Nov 26, 2011, 11:17 PM Jonathan Keats
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Complete pipeline for TGen Saguaro2. This is a parallel version, which launcher each sample as separate PBS jobs. If you have HPC access you can likely use this version with minor fixes specific to your system.  16k v. 2 Nov 27, 2011, 1:14 AM Jonathan Keats
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