[[TOC()]]

= 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 ==

[[Image(CreateGridDirectory.png)]]
   * 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 ==

[[Image(bwaIndexDatabase.png, 50%)]]

== Split fastq file ==

[[Image(splitFastq.png, 50%)]]

== Alignment with BWA on each split file ==

[[Image(BWAparam.png, 50%)]]

== Merge bam files ==

[[Image(MergeIndexSNPcall.png, 50%)]]

== SNP calling with varscan, determine coverage ==

[[Image(Coverage_Varscan_BaseCoverage.png)]]