Workflow Steps and Code Snippets

485 tagged steps and code snippets that match keyword BWA

WES analysis pipeline

shell:
    """
    bwa index {input}
    """

SnakeMake BWA From line 36 of rules/preprocessing.smk

shell:
    """
    gatk SamToFastq -I {input.bam} -F /dev/stdout -INTER true -NON_PF true \
    | \
    bwa mem -p -v 3 -t {threads} -T 0 \
        {input.ref} /dev/stdin - 2> >(tee {log} >&2) \
    | \
    samtools view -Shb -o {output}
    """

SnakeMake SAMtools gatk BWA From line 50 of rules/preprocessing.smk

Whole exome sequencing snakemake workflow based on GATK best practice

shell:
    '''
    gatk --java-options "-Xmx{resources.mem_gb}G -XX:+UseParallelGC -XX:ParallelGCThreads={threads}" \
        SamToFastq \
        -I {input.bam} \
        --FASTQ /dev/stdout \
        --CLIPPING_ATTRIBUTE XT --CLIPPING_ACTION 2 \
        --INTERLEAVE true -NON_PF true | bwa mem -K 100000000 \
        -v 3 {params.bwa_args} -t {threads} -p  -Y {params.index} /dev/stdin | gatk \
        --java-options "-Xmx{resources.mem_gb}G -XX:+UseParallelGC -XX:ParallelGCThreads={threads}" \
        MergeBamAlignment \
        --VALIDATION_STRINGENCY SILENT \
        --EXPECTED_ORIENTATIONS FR \
        --ATTRIBUTES_TO_RETAIN X0 \
        --ALIGNED_BAM /dev/stdin \
        --UNMAPPED_BAM {input.bam} \
        --OUTPUT {output.bam} \
        -R {params.fa} \
        --PAIRED_RUN true \
        --SORT_ORDER "unsorted" \
        --IS_BISULFITE_SEQUENCE false \
        --ALIGNED_READS_ONLY false \
        --CLIP_ADAPTERS false \
        --MAX_RECORDS_IN_RAM 2000000 \
        --ADD_MATE_CIGAR true \
        --MAX_INSERTIONS_OR_DELETIONS -1 \
        --PRIMARY_ALIGNMENT_STRATEGY MostDistant \
        --UNMAPPED_READ_STRATEGY COPY_TO_TAG \
        --ALIGNER_PROPER_PAIR_FLAGS true \
        --UNMAP_CONTAMINANT_READS true {params.warp_workflow_params}
    '''

SnakeMake gatk BWA From line 309 of rules/gatk-bwa-pipeline.smk

High throughput Next Generation Sequencing (NGS) data analysis using Python 3 Snakemake

shell: 
	"""
	~/miniconda2/bin/bwa mem -t {threads} {params} {input.trimmed1} {input.trimmed2} > {output.rnaSam}
	"""

SnakeMake BWA From line 130 of master/Snakefile

A Snakemake workflow to process paired-end RNA-Seq data.

shell:
    '''
    bwa mem -t {threads} {input.rrna} {input.r1} {input.r2} > {output}
    '''

SnakeMake BWA From line 11 of rules/03a_rrna_check.smk

shell:
    '''
    bwa mem -t {threads} {input.rrna} {input.r1} {input.r2} > {output}
    '''

SnakeMake BWA From line 13 of rules/03c_rrna_cleaned_check.smk

EukHeist: Capturing environmental eukaryotic genomes

shell:
    """
    bwa index {input} 2> {log}
    """

SnakeMake BWA From line 270 of master/Snakefile

shell:
    """ 
    bwa mem -t {params.threads} {params.extra} {input.reference} {input.r1} {input.r2} | samtools sort -o {output} - >> {log} 2>&1
    """ 

SnakeMake SAMtools BWA From line 305 of master/Snakefile

Snakemake workflow for analysis of Tara Euk Metagenomes

shell:
    """
    bwa index {input} 2> {log}
    """

SnakeMake BWA From line 294 of master/Snakefile

shell:
    """ 
    bwa mem -t {params.threads} {params.extra} {input.reference} {input.r1} {input.r2} | samtools sort -o {output} - >> {log} 2>&1
    """ 