Changes between Version 2 and Version 3 of CoverageAnalysisPipeline

Timestamp:

Sep 22, 2010 12:37:44 AM (14 years ago)

Author:

Barbera van Schaik

Comment:

--

CoverageAnalysisPipeline

@@ -12 +12 @@
    * Changes the permissions such that it is in-accessible to the group and others
 
-== Create a BWA index on a database ==
+== Create a BWA index on database ==
 
 [[Image(bwaIndexDatabase.png, 50%)]]
+
+Gunzip fasta file. Build BWA index. Tar-gzip the results.
 
 == Split fastq file ==
@@ -20 +22 @@
 [[Image(splitFastq.png, 50%)]]
 
+Splits a large fastq file (gzipped) into several smaller files with the unix command 'split'. The results are uploaded to the directory that is specified in 'gridOutputDir'
+
 == Alignment with BWA on each split file ==
 
 [[Image(BWAparam.png, 50%)]]
+
+Runs BWA with adjustable parameter settings.
+   * Matches sequence reads to a reference database
+   * Convert sai to sam
+   * Convert sam to bam
+   * Sort bam file
+   * Index sorted bam file
+   * Tar-gzip all results. Also the intermediate files
 
 == Merge bam files ==
@@ -28 +40 @@
 [[Image(MergeIndexSNPcall.png, 50%)]]
 
+   * Downloads all bai, bam, sam and tar.gz files from the gridInputDirectory
+   * Gunzip tar the tar.gz files if they are present
+   * Gunzip the reference file (fasta format)
+   * Merge all _sorted.bam files
+   * Build index on this merged file
+   * Call SNPs and make selection. Output in pileup format.
+   * Convert pileup format to bed format
+
 == SNP calling with varscan, determine coverage ==
 
 [[Image(Coverage_Varscan_BaseCoverage.png)]]
+
+   * Creates a pileup file (with samtools pileup -f) Sends the output to Varscan. Calls SNPs, indels and copy number variations.
+   * Calculates coverage per 50kbp
+   * Calculates coverage per base