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alignment-nf

Nextflow pipeline for BAM realignment or fastq alignment

Description

Nextflow pipeline to perform BAM realignment or fastq alignment, with/without local indel realignment and base quality score recalibration.

Dependencies

  1. Nextflow : for common installation procedures see the IARC-nf repository.

Basic fastq alignment

  1. bwa
  2. samblaster
  3. sambamba

BAM files realignment

  1. samtools

Adapter sequence trimming

  1. AdapterRemoval

ALT contigs handling

  1. the k8 javascript execution shell (e.g., available in the bwakit archive)
  2. javascript bwa-postalt.js and the additional fasta reference .alt file from bwakit must be in the same directory as the reference genome file.

Indel realignment

  1. GATK GenomeAnalysisTK.jar
  2. GATK bundle VCF files with lists of indels (recommended: 1000 genomes and Mills gold standard VCFs)

Base quality score recalibration

  1. GATK GenomeAnalysisTK.jar
  2. GATK bundle VCF files with lists of indels and SNVs (recommended: 1000 genomes indels, Mills gold standard indels VCFs, dbsnp VCF)

To avoid installing the previous tools, install Docker. Docker installation is described in the IARC-nf repository.

Input

Type Description
--input_folder a folder with fastq files or bam files

Parameters

  • Mandatory

Name Example value Description
--ref hg19.fasta genome reference with its index files (.fai, .sa, .bwt, .ann, .amb, .pac; in the same directory)
--output_folder . Output folder for aligned BAMs
  • Optional

Name Default value Description
--cpu 8 number of CPUs
--mem 32 memory
--mem_sambamba 1 memory for software sambamba
--RG PL:ILLUMINA sequencing information for aligned (for bwa)
--fastq_ext fastq.gz extension of fastq files
--suffix1 _1 suffix for second element of read files pair
--suffix2 _2 suffix for second element of read files pair
--bed bed file with interval list
--GATK_bundle bundle path to GATK bundle files
--GATK_folder . path to GATK GenomeAnalysisTK.jar file
--js k8 path to javascript interpreter k8
--postaltjs bwa-postalt.js" path to postalignment javascript bwa-postalt.js
  • Flags

Flags are special parameters without value.

Name Description
--help print usage and optional parameters
--trim enable adapter sequence trimming
--indel_realignment perform local indel realignment (GATK)
--recalibration perform quality score recalibration (GATK)
--alt enable alternative contig handling (for reference genome hg38)

Usage

nextflow run iarcbioinfo/alignment-nf --input_folder input --fasta_ref hg19.fasta --out_folder output

Enable adapter trimming

To use the adapter trimming step, you must add the --trim option, as well as satisfy the requirements above mentionned. For example:

nextflow run iarcbioinfo/alignment-nf --input_folder input --fasta_ref reference/hs38DH.fa -out_folder output --trim

Enable ALT mode

To use the alternative contigs handling mode, you must provide the path to an ALT aware genome reference (e.g., hg38) AND add the --alt option, as well as satisfy the requirements above mentionned. For example:

nextflow run iarcbioinfo/alignment-nf --input_folder input --fasta_ref reference/hs38DH.fa --js /user/bin/k8/k8 --postaltjs /user/bin/bwa-0.7.15/bwakit/bwa-postalt.js -out_folder output --alt

Enable local indel realignment

To use the local indel realignment step, you must provide the path to the GATK jar file, the GATK bundle folder, AND add the --indel_realignment option, as well as satisfy the requirements above mentionned. For example:

nextflow run iarcbioinfo/alignment-nf --GATK_bundle GATKbundle/hg19 --input_folder input --fasta_ref reference/hg19.fa --GATK_folder /user/bin7GATK-3.6-0 --out_folder output --indel_realignment

Enable base quality score recalibration

To use the base quality score recalibration step, you must provide the path to the GATK jar file, the GATK bundle folder, a bed file, AND add the --recalibration option, as well as satisfy the requirements above mentionned. For example:

nextflow run iarcbioinfo/alignment-nf --GATK_bundle GATKbundle/hg19 --input_folder input --fasta_ref reference/hg19.fa --GATK_folder /user/bin7GATK-3.6-0 --intervals reference/hg19_intervals.bed --out_folder output --recalibration

Output

Type Description
file.bam BAM files of alignments or realignments
file.bam.bai BAI files of alignments or realignments
file_target_intervals.list list of intervals used
file_recal.table table of scores before recalibration
file_post_recal.table table of scores after recalibration
file_recalibration_plots.pdf before/after recalibration plots

Directed Acyclic Graph

Contributions

Name Email Description
Nicolas Alcala* AlcalaN@fellows.iarc.fr Developer to contact for support
Catherine Voegele VoegeleC@iarc.fr Developer
Vincent Cahais CahaisV@iarc.fr Tester
Alexis Robitaille RobitailleA@students.iarc.fr Tester
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iarcbioinfo
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