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scatter-gather multiple paired-end alignment (bwa)

NicoBxlNicoBxl Member
edited February 2018 in Ask the Cromwell + WDL Team

Hi,

I've a bunch of samples that are described for now in a json like the one below. Each samples is split in multiple R1-R2 fastq pairs i.e. one pair per sequencing lane. I want to align each lane separately and add an RG tag. Than merge all lanes in one merge bam file. What will be the best way to do that using wdl. I already wrote the different tasks for alignment and sam to bam. And the downstream analysis using the merged bam (markduplicates, base quality recalibration, etc..). So some help to bridge the gap woul be great!

Thank you

{
    "sample": [
        {
        "sample_name": "Sample_1",
        "reads":[
            {
                "R1": "S1_l1_R1.fastq.gz",
                "R2": "S1_l1_R2.fastq.gz",
                "lane": "l1"
            },
            {
                "R1": "S1_l2_R1.fastq.gz",
                "R2": "S1_l2_R2.fastq.gz",
                "lane": "l2"
            },
            {
                "R1": "S1_l3_R1.fastq.gz",
                "R2": "S1_l3_R2.fastq.gz",
                "lane": "l3"
            }
            ]
        },
        {
        "sample_name": "Sample_2",
        "reads":[
            {
                "R1": "S2_l1_R1.fastq.gz",
                "R2": "S2_l1_R2.fastq.gz",
                "lane": "l1"
            },
            {
                "R1": "S2_l2_R1.fastq.gz",
                "R2": "S2_l2_R2.fastq.gz",
                "lane": "l2"
            },
            {
                "R1": "S3_l3_R1.fastq.gz",
                "R2": "S3_l3_R2.fastq.gz",
                "lane": "l3"
            }
            ]
        }]
}
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