Changes between Version 2 and Version 3 of CoverageAnalysisPipeline


Ignore:
Timestamp:
Sep 22, 2010 12:37:44 AM (12 years ago)
Author:
Barbera van Schaik
Comment:

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  • CoverageAnalysisPipeline

    v2 v3  
    1212   * Changes the permissions such that it is in-accessible to the group and others
    1313
    14 == Create a BWA index on a database ==
     14== Create a BWA index on database ==
    1515
    1616[[Image(bwaIndexDatabase.png, 50%)]]
     17
     18Gunzip fasta file. Build BWA index. Tar-gzip the results.
    1719
    1820== Split fastq file ==
     
    2022[[Image(splitFastq.png, 50%)]]
    2123
     24Splits 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'
     25
    2226== Alignment with BWA on each split file ==
    2327
    2428[[Image(BWAparam.png, 50%)]]
     29
     30Runs BWA with adjustable parameter settings.
     31   * Matches sequence reads to a reference database
     32   * Convert sai to sam
     33   * Convert sam to bam
     34   * Sort bam file
     35   * Index sorted bam file
     36   * Tar-gzip all results. Also the intermediate files
    2537
    2638== Merge bam files ==
     
    2840[[Image(MergeIndexSNPcall.png, 50%)]]
    2941
     42   * Downloads all bai, bam, sam and tar.gz files from the gridInputDirectory
     43   * Gunzip tar the tar.gz files if they are present
     44   * Gunzip the reference file (fasta format)
     45   * Merge all _sorted.bam files
     46   * Build index on this merged file
     47   * Call SNPs and make selection. Output in pileup format.
     48   * Convert pileup format to bed format
     49
    3050== SNP calling with varscan, determine coverage ==
    3151
    3252[[Image(Coverage_Varscan_BaseCoverage.png)]]
     53
     54   * Creates a pileup file (with samtools pileup -f) Sends the output to Varscan. Calls SNPs, indels and copy number variations.
     55   * Calculates coverage per 50kbp
     56   * Calculates coverage per base