wiki:CoverageAnalysisPipeline

Version 2 (modified by Barbera van Schaik, 14 years ago) (diff)

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Table of Contents

  1. Create grid directory and change permissions
  2. Create a BWA index on a database
  3. Split fastq file
  4. Alignment with BWA on each split file
  5. Merge bam files
  6. SNP calling with varscan, determine coverage

Coverage Analysis Pipeline

TODO. Suggested parties to take this up: Antoine van Kampen, Barbera van Schaik, Silvia D Olabarriaga, Mark Santcroos, AMC

Workflows

Create grid directory and change permissions

WF CreateGridDirectory

  • Creates a directory on the LFC
  • Changes the permissions such that it is in-accessible to the group and others

Create a BWA index on a database

WF Create BWA index on database

Split fastq file

Alignment with BWA on each split file

WF Alignment with BWA

Merge bam files

WF Merge bam files and call SNPs with samtools

SNP calling with varscan, determine coverage

WF call SNPs with varscan, calculate coverage per 50kb and per base

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