Changes between Version 1 and Version 2 of CoverageAnalysisPipeline


Ignore:
Timestamp:
Sep 21, 2010 10:45:04 PM (12 years ago)
Author:
Barbera van Schaik
Comment:

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  • CoverageAnalysisPipeline

    v1 v2  
    22
    33= Coverage Analysis Pipeline =
     4TODO. Suggested parties to take this up: Antoine van Kampen, Barbera van Schaik, Silvia D Olabarriaga, Mark Santcroos, AMC
    45
    5 TODO.
    6 Suggested parties to take this up:
    7 Antoine van Kampen, Barbara van Schaik, AMC
     6= Workflows =
     7
     8== Create grid directory and change permissions ==
     9
     10[[Image(CreateGridDirectory.png)]]
     11   * Creates a directory on the LFC
     12   * Changes the permissions such that it is in-accessible to the group and others
     13
     14== Create a BWA index on a database ==
     15
     16[[Image(bwaIndexDatabase.png, 50%)]]
     17
     18== Split fastq file ==
     19
     20[[Image(splitFastq.png, 50%)]]
     21
     22== Alignment with BWA on each split file ==
     23
     24[[Image(BWAparam.png, 50%)]]
     25
     26== Merge bam files ==
     27
     28[[Image(MergeIndexSNPcall.png, 50%)]]
     29
     30== SNP calling with varscan, determine coverage ==
     31
     32[[Image(Coverage_Varscan_BaseCoverage.png)]]