😎Output files

SvAnna output:

Desctiption: prioritization of possible pathogenic candidate SVs; based on type and length, phenotype conformance and a series of structural pathogenicity scores.

/svanna/sample.html

Combisv output:

Desctiption: finding merged structure variants between cuteSV, SVIM and sniffles2, stored in combisv.vcf; respective combinable results stored in cuteSV_combisv.vcf, SVIM_combisv.vcf, and sniffles_combisv.vcf.

<outdir>/combisv.vcf

<outdir>/cuteSV_combisv.vcf

<outdir>/SVIM_combisv.vcf

<outdir>/sniffles_combisv.vcf

Tldr output:

Desctiption: detecting transposable element those contribute significantly to structureal variations

<outdir>/tldr.table.txt

Straglr output:

Desctiption: finding out possible clinical meaningful tadem repeats based on a preconfigured bed file. The result include basically coordinate, motif, number of repeats, associated gene, etc.

<outdir>/sample.vcf

CuteSV output:

Description: detecting whole genome structural variants using cutesv.

<outdir>/cutesvout.vcf

Sniffles2 output:

Description: detecting whole genome structural variants using sniffles2.

<outdir>/sample_sniffles2.vcf

SVIM output

Description: detecting whole genome structural variants using SVIM.

<outdir>/svimoutput

PanDepth output

Description: estimating coverage and depth for each chromosome using pandepth.

<outdir>/pandepth.chr.stat.gz

Clair3 output

Description: detecting whole genome SNVs and Indels using Clair3.

<outdir>/merge_output.vcf.gz <outdir>/merge_output.vcf.gz.tbi <outdir>/log

Minimap2 AND Samtools output

Description: align the reads, sort and index.

<outdir>/sample_align_sorted.bam <outdir>/sample_align_sorted.bam.bai <outdir>/sample_alignment.bam <outdir>/sample_minimap_aligned.sam