genomic-medicine-sweden/nallo: Output

Aligned reads

Minimap2 is used to map the reads to a reference genome. The aligned reads are sorted, (merged) and indexed using samtools.

Path	Description
aligned_reads/minimap2/{sample}/*.bam	Alignment file in bam format
aligned_reads/minimap2/{sample}/*.bai	Index of the corresponding bam file

If the pipeline is run with phasing, the aligned reads will be happlotagged using the active phasing tool.

Path	Description
{outputdir}/aligned_reads/{sample}/{sample}_haplotagged.bam	BAM file with haplotags
{outputdir}/aligned_reads/{sample}/{sample}_haplotagged.bam.bai	Index of the BAM file

Note

Alignments will only be output without haplotags if phasing is off.

Assembly

Hifiasm is used to assemble genomes. The assembled haplotypes are then comverted to fasta files using gfastats. A deconstructed version of dipcall is to map the assembled haplotypes back to the reference genome.

Path	Description
assembly_haplotypes/gfastats/{sample}/*hap1.p_ctg.fasta.gz	Assembled haplotype 1
assembly_haplotypes/gfastats/{sample}/*hap2.p_ctg.fasta.gz	Assembled haplotype 2
assembly_haplotypes/gfastats/{sample}/*.assembly_summary	Summary statistics
assembly_variant_calling/dipcall/{sample}/*hap1.bam	Assembled haplotype 1 mapped to the reference genome
assembly_variant_calling/dipcall/{sample}/*hap1.bai	Index of the corresponding BAM file for haplotype 1
assembly_variant_calling/dipcall/{sample}/*hap2.bam	Assembled haplotype 2 mapped to the reference genome
assembly_variant_calling/dipcall/{sample}/*hap2.bai	Index of the corresponding BAM file for haplotype 2

Methylation pileups

Modkit is used to create methylation pileups, producing bedMethyl files for both haplotagged and ungrouped reads. Additionaly, methylation information can be viewed in the BAM files, for example in IGV.

Path	Description
methylation/modkit/pileup/phased/{sample}/*.modkit_pileup_phased_*.bed.gz	bedMethyl file with summary counts from haplotagged reads
methylation/modkit/pileup/phased/{sample}/*.modkit_pileup_phased_ungrouped.bed.gz	bedMethyl file for ungrouped reads
methylation/modkit/pileup/unphased/{sample}/*.modkit_pileup.bed.gz	bedMethyl file with summary counts from all reads
methylation/modkit/pileup/unphased/{sample}/*.bed.gz.tbi	Index of the corresponding bedMethyl file

MultiQC

MultiQC generates an HTML report summarizing all samples' QC results and pipeline statistics.

Path	Description
multiqc/multiqc_report.html	HTML report summarizing QC results
multiqc/multiqc_data/	Directory containing parsed statistics
multiqc/multiqc_plots/	Directory containing static report images

Pipeline Information

Nextflow generates reports for troubleshooting, performance, and traceability.

Path	Description
pipeline_info/execution_report.html	Execution report
pipeline_info/execution_timeline.html	Timeline report
pipeline_info/execution_trace.txt	Execution trace
pipeline_info/pipeline_dag.dot	Pipeline DAG in DOT format
pipeline_info/pipeline_report.html	Pipeline report
pipeline_info/software_versions.yml	Software versions used in the run

Phasing

LongPhase, WhatsHap, or HiPhase are used for phasing.

Path	Description
{outputdir}/aligned_reads/{sample}/{sample}_haplotagged.bam	BAM file with haplotags
{outputdir}/aligned_reads/{sample}/{sample}_haplotagged.bam.bai	Index of the BAM file
{outputdir}/phased_variants/{sample}/*.vcf.gz	VCF file with phased variants
{outputdir}/phased_variants/{sample}/*.vcf.gz.tbi	Index of the VCF file
{outputdir}/qc/phasing_stats/{sample}/*.blocks.tsv	Phase block file
{outputdir}/qc/phasing_stats/{sample}/*.stats.tsv	Phasing statistics file

QC

FastQC, cramino, mosdepth, and somalier are used for read quality control.

FastQC

FastQC provides general quality metrics for sequenced reads, including information on quality score distribution, per-base sequence content (%A/T/G/C), adapter contamination, and overrepresented sequences. For more details, refer to the FastQC help pages.

Path	Description
{outputdir}/qc/fastqc/{sample}/*_fastqc.html	FastQC report containing quality metrics
{outputdir}/qc/fastqc/{sample}/*_fastqc.zip	Zip archive with the FastQC report, data files, and plot images

Mosdepth

Mosdepth is used to report quality control metrics such as coverage and GC content from alignment files.

Path	Description
{outputdir}/qc/mosdepth/{sample}/*.mosdepth.global.dist.txt	Cumulative distribution of bases covered for at least a given coverage value, across chromosomes and the whole genome
{outputdir}/qc/mosdepth/{sample}/*.mosdepth.region.dist.txt	Cumulative distribution of bases covered for at least a given coverage value, across regions (if a BED file is used)
{outputdir}/qc/mosdepth/{sample}/*.mosdepth.summary.txt	Mosdepth summary file
{outputdir}/qc/mosdepth/{sample}/*.regions.bed.gz	Depth per region (if a BED file is used)
{outputdir}/qc/mosdepth/{sample}/*.regions.bed.gz.csi	Index of the regions.bed.gz file

Cramino

cramino is used to analyze both phased and unphased reads.

Path	Description
{outputdir}/qc/cramino/phased/{sample}/*.arrow	Read length and quality in Apache Arrow format
{outputdir}/qc/cramino/phased/{sample}/*.txt	Summary information in text format
{outputdir}/qc/cramino/unphased/{sample}/*.arrow	Read length and quality in Apache Arrow format
{outputdir}/qc/cramino/unphased/{sample}/*.txt	Summary information in text format

Somalier

somalier checks relatedness and sex.

Path	Description
{outputdir}/predigree/{project}.ped	PED file updated with somalier-inferred sex
{outputdir}/qc/somalier/relate/{project}/{project}.html	HTML report
{outputdir}/qc/somalier/relate/{project}/{project}.pairs.tsv	Information about sample pairs
{outputdir}/qc/somalier/relate/{project}/{project}.samples.tsv	Information about individual samples

Variants

CNVs

HiFiCNV is used to call CNVs, producing copy number, depth, and MAF tracks for IGV.

Path	Description
cnv_calling/hificnv/{sample}/*.copynum.bedgraph	Copy number in bedgraph format
cnv_calling/hificnv/{sample}/*.depth.bw	Depth track in BigWig format
cnv_calling/hificnv/{sample}/*.maf.bw	Minor allele frequencies in BigWig format
cnv_calling/hificnv/{sample}/*.vcf.gz	VCF file containing CNV variants
cnv_calling/hificnv/{sample}/*.vcf.gz.tbi	Index of the corresponding VCF file

Paralogous genes

Paraphase is used to call paralogous genes.

Path	Description
paraphase/{sample}/*.bam	BAM file with haplotypes grouped by HP
paraphase/{sample}/*.bai	Index of the BAM file
paraphase/{sample}/*.json	Summary of haplotypes and variant calls
paraphase/{sample}_paraphase_vcfs/{sample}_{gene}_vcf	VCF file per gene
paraphase/{sample}_paraphase_vcfs/{sample}_{gene}_vcf.tbi	Index of the VCF file

Repeats

TRGT is used to call repeats:

Path	Description
{outputdir}/repeat_calling/trgt/multi_sample/{project}/*.vcf.gz	Merged VCF file for all samples
{outputdir}/repeat_calling/trgt/multi_sample/{project}/*.vcf.gz.tbi	Index of the VCF file
{outputdir}/repeat_calling/trgt/single_sample/{sample}/*.vcf.gz	VCF file with called repeats for a sample
{outputdir}/repeat_calling/trgt/single_sample/{sample}/*.vcf.gz.tbi	Index of the VCF file
{outputdir}/repeat_calling/trgt/single_sample/{sample}/*.bam	BAM file with sorted spanning reads
{outputdir}/repeat_calling/trgt/single_sample/{sample}/*.bai	Index of the BAM file

Stranger is used to annotate them:

Path	Description
{outputdir}/repeat_annotation/stranger/{sample}/*.vcf.gz	Annotated VCF file
{outputdir}/repeat_annotation/stranger/{sample}/*.vcf.gz.tbi	Index of the annotated VCF file

SNVs

DeepVariant is used to call variants, while bcftools and GLnexus are used for merging variants.

Note

Variants are only output without annotation and ranking if these subworkflows are turned off.

Path	Description
snvs/single_sample/{sample}/{sample}_snv.vcf.gz	VCF file containing called variants with alternative genotypes for a sample
snvs/single_sample/{sample}/{sample}_snv.vcf.gz.tbi	Index of the corresponding VCF file
snvs/multi_sample/{project}/{project}_snv.vcf.gz	VCF file containing called variants for all samples
snvs/multi_sample/{project}/{project}_snv.vcf.gz.tbi	Index of the corresponding VCF file
snvs/stats/single_sample/*.stats.txt	Variant statistics

echtvar and VEP are used for annotating SNVs, while CADD is used to annotate INDELs with CADD scores.

Note

Variants are only output without ranking if that subworkflows are turned off.

Path	Description
databases/echtvar/encode/{project}/*.zip	Database with allele frequency (AF) and allele count (AC) for all samples
snvs/single_sample/{sample}/{sample}_snv_annotated.vcf.gz	VCF file containing annotated variants with alternative genotypes for a sample
snvs/single_sample/{sample}/{sample}_snv_annotated.vcf.gz.tbi	Index of the annotated VCF file
snvs/multi_sample/{project}/{project}_snv_annotated.vcf.gz	VCF file containing annotated variants for all samples
snvs/multi_sample/{project}/{project}_snv_annotated.vcf.gz.tbi	Index of the annotated VCF file

GENMOD is used to rank the annotated SNVs and INDELs.

Path	Description
snvs/single_sample/{sample}/{sample}_snv_annotated_ranked.vcf.gz	VCF file with annotated and ranked variants for a sample
snvs/single_sample/{sample}/{sample}_snv_annotated_ranked.vcf.gz.tbi	Index of the ranked VCF file
snvs/multi_sample/{project}/{project}_snv_annotated_ranked.vcf.gz	VCF file with annotated and ranked variants for all samples
snvs/multi_sample/{project}/{project}_snv_annotated_ranked.vcf.gz.tbi	Index of the ranked VCF file

SVs

Severus or Sniffles is used to call structural variants, and SVDB is used to merge variants within and between samples.

Note

Variants are only output without annotation if that subworkflow is turned off.

Path	Description
svs/multi_sample/{project}/{project}_svs.vcf.gz	VCF file with merged structural variants for all samples
svs/multi_sample/{project}/{project}_svs.vcf.gz.tbi	Index of the merged VCF file
svs/single_sample/{sample}/*.vcf.gz	VCF file with merged structural variants for a single sample
svs/single_sample/{sample}/*.vcf.gz.tbi	Index of the VCF file

SVDB and VEP are used to annotate structural variants.

Path	Description
svs/multi_sample/{project}/{project}_svs_annotated.vcf.gz	VCF file with annotated merged structural variants for all samples
svs/multi_sample/{project}/{project}_svs_annotated.vcf.gz.tbi	Index of the annotated VCF file
svs/single_sample/{sample}/*.vcf_annotated.gz	VCF file with annotated structural variants for a single sample
svs/single_sample/{sample}/*.vcf_annotated.gz.tbi	Index of the annotated VCF file