iarcbioinfo/bqsr-nf
Automatic build for BQSR nextflow pipeline at https://github.com/IARCbioinfo/BQSR-nf/
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iarcbioinfo/bqsr-nf repository overview
BQSR-nf
Nextflow script for base quality score recalibration of bam files using GATK
Nextflow pipeline for base quality score recalibration with GATK processing
Decription
Nextflow pipeline for base quality score recalibration and quality control
Dependencies
-
Nextflow: for common installation procedures see the IARC-nf repository.
-
GATK4 must be in the PATH variable
-
GATK bundle VCF files with lists of indels and SNVs (recommended: 1000 genomes indels, dbsnp VCF)
You can provide a config file to customize the multiqc report (see https://multiqc.info/docs/#configuring-multiqc).
Input
| Type | Description |
|---|---|
| --input_folder | a folder with bam files |
Parameters
-
Mandatory
| Name | Example value | Description |
|---|---|---|
| --ref | ref.fa | reference genome fasta file for GATK |
-
Optional
| Name | Default value | Description |
|---|---|---|
| --cpu | 2 | number of CPUs |
| --mem | 32 | memory for mapping |
| --output_folder | . | output folder for aligned BAMs |
| --snp_vcf | dbsnp.vcf | VCF file with known variants for GATK BQSR |
| --indel_vcf | Mills_100G_indels.vcf | VCF file with known indels for GATK BQSR |
| --multiqc_config | null | config yaml file for multiqc |
-
Flags
| Name | Description |
|---|---|
| --help | print usage and optional parameters |
Usage
To run the pipeline on a series of bam files in folder bam, a reference genome with indexes at ref.fa, and known snps and indels from the gatk bundle, one can type:
nextflow run iarcbioinfo/BQSR-nf --input_folder bam --ref ref.fa --snp_vcf GATK_bundle/dbsnp_146.hg38.vcf.gz --indel_vcf GATK_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
Output
| Type | Description |
|---|---|
| BAM/file.bam | BAM files of alignments or realignments |
| BAM/file.bam.bai | BAI files of alignments or realignments |
| QC/multiqc_BQSR_report.html | multiqc report |
| QC/multiqc_BQSR_report_data | folder with data used to compute multiqc report |
| QC/BAM/BQSR/file_recal.table | table of scores before recalibration |
| QC/BAM/BQSR/file_post_recal.table | table of scores after recalibration |
| QC/BAM/BQSR/file_recalibration_plots.pdf | before/after recalibration plots |
The output_folder directory contains two subfolders: BAM and QC
Directed Acyclic Graph
Contributions
| Name | Description | |
|---|---|---|
| Nicolas Alcala* | [email protected] | Developer to contact for support |
Tag summary
Content type
Image
Digest
Size
1.3 GB
Last updated
almost 7 years ago
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