CFseq analysis pipeline scripts.

Lefterova MI, Shen P, Odegaard JI, et al. Next-generation molecular testing of newborn dried blood spots for cystic fibrosis. J Mol Diagn (http://jmd.amjpathol.org).

The pipeline uses the following software and was designed using the version numbers listed.
All software are freely available for non-commercial use.

• ANNOVAR:

  • http://www.openbioinformatics.org/annovar/
  • release 141112

• BWA:

  • http://bio-bwa.sourceforge.net
  • version 0.7.12

• FreeBayes:

  • https://github.com/ekg/freebayes
  • version v0.9.21-7-g7dd41db

• GATK:

  • http://www.broadinstitute.org/gatk/
  • version 3.3

• Picard

  • http://broadinstitute.github.io/picard/
  • version 1.124

• SAMtools:

  • http://www.htslib.org
  • version 1.1

• cross_match/phrap:

  • http://www.phrap.org/phredphrapconsed.html
  • release 990329

• pysam:

  • https://pypi.python.org/pypi/pysam
  • version 0.8.4

Place these executables in the bin directory:

• annotate_variation.pl - from ANNOVAR
• convert2annovar.pl - from ANNOVAR
• table_annovar.pl - from ANNOVAR
• bwa
• cross_match.manyreads
• freebayes
• GenomeAnalysisTK.jar
• picard.jar
• samtools

Download the 'refGene' database from ANNOVAR to resources/annovar_dbs.