Changes between Version 2 and Version 3 of SnpCallingPipeline


Ignore:
Timestamp:
Sep 12, 2010 11:38:01 PM (11 years ago)
Author:
Morris Swertz
Comment:

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  • SnpCallingPipeline

    v2 v3  
    1212
    1313This process involves all needed steps to prepare the raw sequencing reads for an alignment using BWA. These steps are all conducted using PICARD. An overview of the steps can be found in Appendix A.
    14 
    1514=== 1) Read converting ===
    1615
    1716This step involves converting the output from the Illumina GAII, FASTQ format, to binary SAM format (BAM). To do this !FastqToSam.jar can be used. The following command was used:
    1817
     18{{{
    1919java -jar !FastqToSam.jar FASTQ=../testrun/s_2_sequence041090.txt QUALITY_FORMAT=Illumina OUTPUT=../testrun/s_2_sequence.bam SAMPLE_NAME=s_2_test_sample PLATFORM_UNIT=barcode_13434HWUSIsomething PLATFORM=illumina SORT_ORDER=coordinate
     20}}}
    2021
    2122It is also possible to convert raw BUSTARD data to BAM using !BustardToSam.jar. The advantage of this tool is the multiple lane input, in theory all lanes from one flow cell can be converted parallel. To remove possible linkers from reads a tool named !ExtractIlluminaBarcodes.jar can be used. Since there isn’t any data including these barcodes this and the !BustardToSam haven’t been tested yet.