Oct 02, 2023

Sniffles2 methods

DOI
https://dx.doi.org/10.17504/protocols.io.14egn34qyl5d/v1
  • 1Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA;
  • 2Department of Molecular and Human Genetics, Baylor College of Medicine, TX, USA;
  • 3Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA;
  • 4Department of Computer Science, Rice University, 6100 Main Street, Houston, TX, USA
Luis F Paulin
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DOI: https://dx.doi.org/10.17504/protocols.io.14egn34qyl5d/v1
Protocol Citation: Moritz Smolka, Luis Paulin, Fritz J Sedlazeck 2023. Sniffles2 methods. protocols.io https://dx.doi.org/10.17504/protocols.io.14egn34qyl5d/v1
Manuscript citation:
License: This is an open access  protocol  distributed under the terms of the  Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: September 29, 2023
Last Modified: October 02, 2023
Protocol  Integer ID: 88599
Keywords: complex genomic alteration, remarkable diversity within the cingulate cortex, genotyped vcf file, causative svs around mecp2, gene, read structural variation, multiple system atrophy patient brain, sequencing, sequencing technology, detection of mosaic sv, cingulate cortex, identified sv, versatility of sniffles2, svs from the mosaic, multiple mosaic sv, art sv caller across different coverage, vcf file, mosaic sv, mecp2
Funders Acknowledgements:
National Institute of General Medical Sciences
Grant ID: R01 GM132589
Intramural Research Program of the National Institutes of Health
Grant ID: 1ZIANS003154
MSA Trust
Grant ID: MSA Trust
NIH grants
Grant ID: UM1HG008898, 1U01HG011758-01, U01 AG058589, 1UG3NS132105-01 and PO 75N95021P00215
Center for Alzheimer’s and Related Dementias (CARD)
Grant ID: project ZO1 AG000538-02
Aligning Science Across Parkinson’s through the Michael J. Fox Foundation for Parkinson’s Research (MJFF)
Grant ID: 000430
Abstract
Long-read Structural Variation (SV) calling remains a challenging but highly accurate way to identify complex genomic alterations. Here, we present Sniffles2, which is faster and more accurate than state-of-the-art SV caller across different coverages, sequencing technologies, and SV types. Furthermore, Sniffles2 solves the problem of family- to population-level SV calling to produce fully genotyped VCF files by introducing a gVCF file concept. Across 11 probands, we accurately identified causative SVs around MECP2, including highly complex alleles with three overlapping SVs. Sniffles2 also enables the detection of mosaic SVs in bulk long-read data. As a result, we successfully identified multiple mosaic SVs across a multiple system atrophy patient brain. The identified SV showed a remarkable diversity within the cingulate cortex, impacting both genes involved in neuron function and repetitive elements. In summary, we demonstrate the utility and versatility of Sniffles2 to identify SVs from the mosaic to population levels.

Before start
Requirements
  • Python >= 3.7
  • pysam
Tested on:
  • Linux CentOS Stream 8
  • python==3.9.5
  • pysam==0.16.0.1
Sniffles2 methodology
Installation

Command
Sniffles install pip
pip install sniffles

Command
Sniffles install conda
conda install sniffles=2.2

Sniffles single sample SV calling
Command
Sniffles call
sniffles --input mapped_input.bam --vcf output.vcf.gz --snf output.snf

Sniffles population SV calling
Command
Sniffles population
sniffles --input sample1.bam --vcf sample1.vcf.gz --snf sample1.snf

sniffles --input sample2.bam --vcf sample2.vcf.gz --snf sample2.snf

sniffles --input sampleN.bam --vcf sampleN.vcf.gz --snf sampleN.snf

sniffles --input sample1.snf sample2.snf sampleN.snf --vcf multisample.vcf.gz

Sniffles low-frequency (mosaic) SV calling
Command
Sniffles mosaic
sniffles --input sample.bam --vcf sample_mosaic_sv.vcf.gz --mosaic

Optional suggested parameters
Command
Sniffles optional suggested
# will include the sequence of deletion
--reference reference.fasta

# will output the read names used for every SV
----output-rnames

# will use tandem repeat annotation for the reference genome. Provided for human GRCh37 and GRCh38
--tandem-repeats repeats.bed

Sniffles genotyping (force-callling) will determine the genotypes for all SVs in the given input .vcf fil
Command
Sniffles genotyping
sniffles --input mapped_input.bam --vcf output.vcf.gz --snf output.snf --genotype-vcf known_sv.vcf.gz

Long reads alignment
Minimap2
MINIMAP_PRESET used are: map-ont for Oxford Nanopore and map-hifi for PacBio HiFi and map-pb for PacBio CLR
REFERENCE is either human GRCh37 or GRCh38 with no alt/decoy chromosomes
READS are fastq/compressed-fastq files
OUT is the sample name/identification
Command
Long reads alignment with minimap2 (Linux: CentOS Stream 8)
minimap2 \
  -ax ${MINIMAP_PRESET} \
  -t 8  -Y --MD  \
  ${REFERENCE} \
  ${READS} | samtools sort -m 2G - > ${OUT}.bam

LRA
READS are gzip-compressed-fastq files
LRA_PRESET used are: -ONT for Oxford Nanopore and -CCS for PacBio HiFi and -CLRfor PacBio CLR
REFERENCE is either human GRCh37 or GRCh38 with no alt/decoy chromosomes
OUTFORMAT is s for SAM
OUT is the sample name/identification
Command
Long read alignment with LRA (Linux: CentOS Stream 8)
gzip-cd ${READS} | lra align ${LRA_PRESET} -t 8 -p ${OUTFORMAT} --noMismatch ${REFERENCE} /dev/stdin | samtools view -hb - | samtools sort - > ${OUT}.bam"

Benchmarking methodology

HG002 SV calling for the following technologies and coverage:
Oxford Nanopore Technologies: 5x, 10x, 20x, 30x and 50x
PacBio HiFi: 5x, 10x, 20x, 30x
with default parameters
Command
HG002 ONT SV calling default parameters (Linux: CentOS Stream 8)
for genome in "grch37" "grch38"; do
    # Sniffles2
    sniffles2 --tandem-repeats human_${genome}.trf.bed -i hg002_ont_${genome}.bam -v sniffles2_hg002_ont_${genome}.vcf -t 8 --reference ${genome}.fasta
    # Sniffles1
    sniffles1 -m hg002_ont_${genome}.bam -v sniffles1_hg002_ont_${genome}.vcf -t 8
    # cuteSV
    cuteSV --max_cluster_bias_INS 100 --diff_ratio_merging_INS 0.3 --max_cluster_bias_DEL 100 --diff_ratio_merging_DEL 0.3 --genotype -t 8 hg002_ont_${genome}.bam ${genome}.fasta cutesv_hg002_ont_${genome}.vcf tmp
    # pbsv
    bash -c "pbsv discover -s hg2 --tandem-repeats human_${genome}.trf.bed hg002_ont_${genome}.bam pbsv.svsig.gz && pbsv call -j 8 ${genome}.fasta pbsv.svsig.gz pbsv_hg002_ont_${genome}.vcf" 
    # SVIM
    svim alignment --sequence_alleles tmp hg002_ont_${genome}.bam ${genome}.fasta && mv variants.vcf svim_hg002_ont_${genome}.vcf
done

Command
HG002 HiFi SV calling default parameters (Linux: CentOS Stream 8)
for genome in "grch37" "grch38"; do
    # Sniffles2
    sniffles2  --tandem-repeats human_${genome}.trf.bed -i hg002_hifi_${genome}.bam -v sniffles2_hg002_hifi_${genome}.vcf -t 8 --reference ${genome}.fasta
    # Sniffles1
    sniffles1  -m hg002_hifi_${genome}.bam -v sniffles1_hg002_hifi_${genome}.vcf -t 8
    # cuteSV
    cuteSV --max_cluster_bias_INS 1000 --diff_ratio_merging_INS 0.9 --max_cluster_bias_DEL 1000 --diff_ratio_merging_DEL 0.5  --genotype -t 8 hg002_hifi_${genome}.bam ${genome}.fasta cutesv_hg002_hifi_${genome}.vcf tmp
    # pbsv
    bash -c "pbsv discover -s hg2 --tandem-repeats human_${genome}.trf.bed hg002_hifi_${genome}.bam pbsv.svsig.gz && pbsv call -j 8 --ccs  ${genome}.fasta pbsv.svsig.gz pbsv_hg002_hifi_${genome}.vcf" 
    # SVIM
    svim alignment --sequence_alleles tmp hg002_hifi_${genome}.bam ${genome}.fasta && mv variants.vcf svim_hg002_hifi_${genome}.vcf
done


HG002 SV calling for the following technologies and coverage:
Oxford Nanopore Technologies: 5x, 10x, 20x, 30x and 50x
PacBio HiFi: 5x, 10x, 20x, 30x
with sensitive parameters
Command
HG002 ONT SV calling sensitive parameters (Linux: CentOS Stream 8)
for genome in "grch37" "grch38"; do
    # Sniffles1
    sniffles1 -s 2 -m hg002_ont_${genome}.bam -v sniffles1_hg002_ont_${genome}.vcf -t 8
    # cuteSV
    cuteSV --max_cluster_bias_INS 100 --diff_ratio_merging_INS 0.3 --max_cluster_bias_DEL 100 --diff_ratio_merging_DEL 0.3 -s 2 --genotype -t 8 hg002_ont_${genome}.bam ${genome}.fasta cutesv_hg002_ont_${genome}.vcf tmp
    # pbsv
    bash -c "pbsv discover -s hg2 --tandem-repeats human_${genome}.trf.bed hg002_ont_${genome}.bam pbsv.svsig.gz && pbsv call -j 8  -A 2 ${genome}.fasta pbsv.svsig.gz pbsv_hg002_ont_${genome}.vcf" 
    # SVIM
    svim alignment --sequence_alleles tmp hg002_ont_${genome}.bam ${genome}.fasta && mv variants.vcf svim_hg002_ont_${genome}.vcf
done

Command
HG002 HiFi SV calling sensitive parameters (Linux: CentOS Stream 8 )
for genome in "grch37" "grch38"; do
    # Sniffles1
    sniffles1 -s 2 -m hg002_hifi_${genome}.bam -v sniffles1_hg002_hifi_${genome}.vcf -t 8
    # cuteSV
    cuteSV --max_cluster_bias_INS 1000 --diff_ratio_merging_INS 0.9 --max_cluster_bias_DEL 1000 --diff_ratio_merging_DEL 0.5 -s 2 --genotype -t 8 hg002_hifi_${genome}.bam ${genome}.fasta cutesv_hg002_hifi_${genome}.vcf tmp
    # pbsv
    bash -c "pbsv discover -s hg2 --tandem-repeats human_${genome}.trf.bed hg002_hifi_${genome}.bam pbsv.svsig.gz && pbsv call -j 8 --ccs -A 2 ${genome}.fasta pbsv.svsig.gz pbsv_hg002_hifi_${genome}.vcf" 
    # SVIM
    svim alignment --sequence_alleles tmp hg002_hifi_${genome}.bam ${genome}.fasta && mv variants.vcf _hg002_hifi_${genome}.vcf
done


SV benchmark comparison to Genome in a Bottle SV dataset v0.6 using truvari 2.1 following the GIAB recommended parameters
Command
GRCh37 / GIAB v0.6 SV benchmark (Truvari bench) (Linux: CentOS Stream 8)
for longreads in "ont" "hifi"; do
    truvari bench -b HG002_SVs_Tier1_v0.6.vcf.gz -c hg002_${longreads}_grch37.vcf.gz -o truvari_bench_${longreads} -f grch37.fasta --includebed HG002_SVs_Tier1_v0.6.bed --passonly --giabreport
done
SV benchmark comparison to Genome in a Bottle SV Challenging Medical Relevant Genes (CMRG) v0.1 using truvari 2.1 following the GIAB recommended parameters
Command
GRCh38 / Challenging Medical Relevant Genes (CMRG) benchmark (Truvari bench) (Linux: CentOS Stream 8)
for longreads in "ont" "hifi"; do
    truvari bench -b HG002_CMRG_v0.01.vcf.gz -c hg002_${longreads}_grch38.vcf.gz -o truvari_bench -f grch38.fa --includebed HG002_GRCh38_CRMG_v0.01.bed --passonly
done

Simulation of low-frequency SVs
Low-frequency SV simulation
We used 
samtools view --subsample
 to create subset of reads fo HG002 and HG00733 at the following concentrations:
HG002 coverageHG002 proportionHG00733 coverageHG00733 proportion
57%6393%
710%6390%
1014%6086%
1521%5579%
2028%5072%
HG002 reads: https://labs.epi2me.io/gm24385_q20_2021.10/
HG002 variants: https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG002_NA24385_son/NIST_SV_v0.6/HG002_SVs_Tier1_v0.6.vcf.gz
HG00733 reads: https://www.internationalgenome.org/data-portal/search?q=HG00733
HG00733 variants: https://ftp.hgsc.bcm.edu/Software/Truvari/3.1/sample_vcfs/hg19/li/HG00733.vcf.gz
Read alignment was performed as in step 7

SV calling with Sniffles2 and cuteSV

Command
Low-frequency SV calling benchmark (Linux: CentOS Stream 8)
# Sniffles2 mosaic
sniffles2 --tandem-repeats human_hs37d5.trf.bed -i hg002_hg00733.bam -t 8 --reference grch37.fasta -v sniffles2_hg002_hg00733_mosaic.vcf --mosaic

# Sniffles2 germline (default)
sniffles2 --tandem-repeats human_hs37d5.trf.bed -i hg002_hg00733.bam -t 8 --reference grch37.fasta -v sniffles2_hg002_hg00733_germline.vcf

# cuteSV
cuteSV --max_cluster_bias_INS 100 --diff_ratio_merging_INS 0.3 --max_cluster_bias_DEL 100 --diff_ratio_merging_DEL 0.3 --genotype -t 8 hg002_hg00733.bam  grch37.fasta  cute_SV_hg002_hg00733.vcf tmp
SV benchmark
We then used the SV from the GIAB v0.6 benchmark (see step 11) and compared the three call sets: Sniffles germline, Sniffles mosaic and cuteSV. For Sniffles mosaic we also filtered GIAB v0.6 benchmark based on the variant allele frequency (VAF) range that Sniffles2 mosaic mode uses (VAF 5%-20%) to compute the adjusted recall.
Mendelian inconsistency benchmark in population mode
Read alignment was don as in step 7
Sniffles2 SV calling was done as in step 3
cuteSV SV calling was done as in step 10 for Oxford Nanopore data for each sample
Next SURVIVOR was used to merge the SV calls from the three samples
Command
SURVIVOR merge (Linux: CentOS Stream 8)
ls cutesv_hg002_grch37.vcf cutesv_hg003_grch37.vcf cutesv_hg004_grch37.vcf > trio_samples.list
survivor merge trio_samples.list 1000 1 1 0 0 50 cuteSV_trio_grch37.vcf

An additional step was performed for cuteSV which consists in genotyping/force-calling the SV from the merged VCF, to then merge again with SURVIVOR
Command
cuteSV force-call and merge (Linux: CentOS Stream 8)
# Calling
for sample_id in "hg002" "hg003" "hg004"; do
    cuteSV --max_cluster_bias_INS 100 --diff_ratio_merging_INS 0.3 --max_cluster_bias_DEL 100 --diff_ratio_merging_DEL 0.3 -s 2 --genotype -t 8 ${sample_id}_grch37.bam grch37.fasta cutesv_${sample_id}_grch37_force.vcf tmp -Ivcf cuteSV_trio_grch37.vcf
done

# Merge
ls cutesv_hg002_grch37_force.vcf cutesv_hg003_grch37_force.vcf cutesv_hg004_grch37_force.vcf > trio_samples_force.list
survivor merge trio_samples_force.list 1000 1 1 0 0 50 cuteSV_trio_grch37_force.vcf

Mendelian consistency test with bcftools's mendelian plugin with the three output files:
Sniffles2 population merge (step 18), cuteSV (step 19) and cuteSV force-called (step 20)
Command
bcftools mendelian consistency (Linux: CentOS Stream 8)
# Sniffles2 population
bcftools +mendelian sniffles2_trio_grch37.vcf.gz -t hg004,hg003,hg002

# cuteSV vanilla
bcftools +mendelian cuteSV_trio_grch37.vcf -t hg004,hg003,hg002

# cuteSV force-called
bcftools +mendelian cuteSV_trio_grch37_force.vcf -t hg004,hg003,hg002

Chromosome X disorder patient analysis
We called all samples as in step 3 (Sniffles2 population SV calling) and subsequently merged them (step 3). We used the resulting fully-genotyped population VCF file of the rest of the analysis.

Next, we filtered out SV if they were in either of the following categories:
  • SV < 10kb
  • SV present in either a mother or father based on the sample identification and SUPP_VEC (see below)
  • SV in an autosome

We ended up with SV that were only present in the probands and that were likely causative of the observed phenotype.
Filtering was done with bcftools view and a custom python script "sniffles2_vcf_parser.py"found in https://github.com/smolkmo/Sniffles2-Supplement and https://zenodo.org/record/8122060

The SUPP_VEC is a field in the INFO section of the VCF file that denotes the presence/absence of a genetic variant (in our case Structural Variant, SV) in the sample for the sample position/index
For samples A B and C, the SUPP_VEC=101 means that the genetic variant is present in samples A and C
Protocol references
Comprehensive Structural Variant Detection: From Mosaic to Population-Level
Moritz Smolka, Luis F. Paulin, et al doi:https://doi.org/10.1101/2022.04.04.4870555

Li, H. New strategies to improve minimap2 alignment accuracy. Bioinformatics (2021) doi:10.1093/bioinformatics/btab705.

Danecek, P. et al. Twelve years of SAMtools and BCFtools. Gigascience 10, (2021).

Sedlazeck, F. J. et al. Accurate detection of complex structural variations using single- molecule sequencing. Nat. Methods 15, 461–468 (2018).

Jiang, T. et al. Long-read-based human genomic structural variation detection with cuteSV. Genome Biol. 21, 189 (2020).

PacificBiosciences. GitHub - PacificBiosciences/pbsv: pbsv - PacBio structural variant (SV) calling and analysis tools. GitHub https://github.com/PacificBiosciences/pbsv.

Heller, D. & Vingron, M. SVIM: structural variant identification using mapped long reads. Bioinformatics 35, 2907–2915 (2019)

English, A. C., Menon, V. K., Gibbs, R., Metcalf, G. A. & Sedlazeck, F. J. Truvari: Refined Structural Variant Comparison Preserves Allelic Diversity.Genome Biol 23, 271 (2022)

Zook, J. M. et al. A robust benchmark for detection of germline large deletions and insertions. Nat. Biotechnol. 38, 1347–1355 (2020).

Jeffares, D. C. et al. Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast. Nat. Commun. 8, 14061 (2017)