multiqc

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        Download the raw data used to create the plots in this report below:

        Note that additional data was saved in multiqc_multiqc_report_data when this report was generated.

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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        Tool Citations

        Please remember to cite the tools that you use in your analysis.

        To help with this, you can download publication details of the tools mentioned in this report:

        About MultiQC

        This report was generated using MultiQC, version 1.17

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        multiqc

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        This report has been generated by the nf-core/sarek analysis pipeline. For information about how to interpret these results, please see the documentation.

        Report generated on 2024-03-30, 00:41 UTC based on data in: /home/wajid/nextflow/work/cf/4074a2b95ddde23b89d2093e72b438

        General Statistics

        Showing 1/1 rows and 4/5 columns.
        Sample NameVarsSNPIndelTs/Tv
        1HQ.haplotypecaller.filtered
        618899
        537719
        81245
        2.02

        Bcftools

        Version: 1.17

        Bcftools contains utilities for variant calling and manipulating VCFs and BCFs.DOI: 10.1093/gigascience/giab008.

        Variant Substitution Types

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        Variant Quality

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        Indel Distribution

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        Variant depths

        Read depth support distribution for called variants

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        Vcftools

        Vcftools is a program for working with and reporting on VCF files.DOI: 10.1093/bioinformatics/btr330.

        TsTv by Count

        Plot of TSTV-BY-COUNT - the transition to transversion ratio as a function of alternative allele count from the output of vcftools TsTv-by-count.

        Transition is a purine-to-purine or pyrimidine-to-pyrimidine point mutations. Transversion is a purine-to-pyrimidine or pyrimidine-to-purine point mutation. Alternative allele count is the number of alternative alleles at the site. Note: only bi-allelic SNPs are used (multi-allelic sites and INDELs are skipped.) Refer to Vcftools's manual (https://vcftools.github.io/man_latest.html) on --TsTv-by-count

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        TsTv by Qual

        Plot of TSTV-BY-QUAL - the transition to transversion ratio as a function of SNP quality from the output of vcftools TsTv-by-qual.

        Transition is a purine-to-purine or pyrimidine-to-pyrimidine point mutations. Transversion is a purine-to-pyrimidine or pyrimidine-to-purine point mutation. Quality here is the Phred-scaled quality score as given in the QUAL column of VCF. Note: only bi-allelic SNPs are used (multi-allelic sites and INDELs are skipped.) Refer to Vcftools's manual (https://vcftools.github.io/man_latest.html) on --TsTv-by-qual

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        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        SoftwareVersion
        Bcftools1.17

        nf-core/sarek Methods Description

        Suggested text and references to use when describing pipeline usage within the methods section of a publication.

        Methods

        Data was processed using nf-core/sarek v3.4.0 (doi: 10.12688/f1000research.16665.2, 10.1101/2023.07.19.549462, 10.5281/zenodo.3476425) of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

        The pipeline was executed with Nextflow v24.02.0-edge (Di Tommaso et al., 2017) with the following command:

        nextflow run nf-core/sarek -r 3.4.0 -profile docker -params-file nf-params.json --max_memory 30.GB

        References

        • Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
        • Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
        • Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
        • da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192
        Notes:
        • The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
        • You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.

        nf-core/sarek Software Versions

        are collected at run time from the software output.

        Process Name Software Version
        BAM_TO_CRAM samtools 1.17
        BCFTOOLS_STATS bcftools 1.17
        CNNSCOREVARIANTS gatk4 4.4.0.0
        CREATE_INTERVALS_BED gawk 5.1.0
        CUSTOM_DUMPSOFTWAREVERSIONS python 3.12.0
        yaml 6.0.1
        FILTERVARIANTTRANCHES gatk4 4.4.0.0
        GATK4_HAPLOTYPECALLER gatk4 4.4.0.0
        MERGE_HAPLOTYPECALLER gatk4 4.4.0.0
        TABIX_BGZIPTABIX_INTERVAL_COMBINED tabix 1.12
        TABIX_BGZIPTABIX_INTERVAL_SPLIT tabix 1.12
        VCFTOOLS_TSTV_COUNT vcftools 0.1.16
        Workflow Nextflow 24.02.0-edge
        nf-core/sarek 3.4.0

        nf-core/sarek Workflow Summary

        - this information is collected when the pipeline is started.

        Core Nextflow options

        revision
        3.4.0
        runName
        friendly_magritte
        containerEngine
        docker
        launchDir
        /home/wajid/nextflow
        workDir
        /home/wajid/nextflow/work
        projectDir
        /home/wajid/.nextflow/assets/nf-core/sarek
        userName
        wajid
        profile
        docker
        configFiles
        N/A

        Input/output options

        input
        /home/wajid/nextflow/results/csv/recalibrated.csv
        step
        variant_calling
        outdir
        /home/wajid/nextflow/results

        Main options

        wes
        true
        intervals
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/intervals/wgs_calling_regions_noseconds.hg38.bed
        tools
        haplotypecaller

        Variant Calling

        cf_chrom_len
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/Length/Homo_sapiens_assembly38.len

        Reference genome options

        ascat_genome
        hg38
        ascat_alleles
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/G1000_alleles_hg38.zip
        ascat_loci
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/G1000_loci_hg38.zip
        ascat_loci_gc
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/GC_G1000_hg38.zip
        ascat_loci_rt
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/RT_G1000_hg38.zip
        bwa
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/BWAIndex/
        bwamem2
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/BWAmem2Index/
        chr_dir
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/Chromosomes
        dbsnp
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz
        dbsnp_tbi
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi
        dbsnp_vqsr
        --resource:dbsnp,known=false,training=true,truth=false,prior=2.0 dbsnp_146.hg38.vcf.gz
        dict
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict
        dragmap
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/dragmap/
        fasta
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
        fasta_fai
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai
        germline_resource
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz
        germline_resource_tbi
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz.tbi
        known_indels
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz
        known_indels_tbi
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi
        known_indels_vqsr
        --resource:gatk,known=false,training=true,truth=true,prior=10.0 Homo_sapiens_assembly38.known_indels.vcf.gz --resource:mills,known=false,training=true,truth=true,prior=10.0 Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
        known_snps
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000G_omni2.5.hg38.vcf.gz
        known_snps_tbi
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000G_omni2.5.hg38.vcf.gz.tbi
        known_snps_vqsr
        --resource:1000G,known=false,training=true,truth=true,prior=10.0 1000G_omni2.5.hg38.vcf.gz
        mappability
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/Control-FREEC/out100m2_hg38.gem
        ngscheckmate_bed
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/NGSCheckMate/SNP_GRCh38_hg38_wChr.bed
        pon
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000g_pon.hg38.vcf.gz
        pon_tbi
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000g_pon.hg38.vcf.gz.tbi
        sentieon_dnascope_model
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/Sentieon/SentieonDNAscopeModel1.1.model
        snpeff_db
        105
        snpeff_genome
        GRCh38
        vep_genome
        GRCh38
        vep_species
        homo_sapiens
        vep_cache_version
        110

        Max job request options

        max_cpus
        3
        max_memory
        30.GB

        Generic options

        multiqc_title
        multiqc
        validationLenientMode
        true

        MultiQC v1.17 - Written by Phil Ewels, available on GitHub.

        This report uses HighCharts, jQuery, jQuery UI, Bootstrap, FileSaver.js and clipboard.js.