Snippy
Rapid haploid variant calling and core genome alignment
Author
Torsten Seemann
Synopsis
Snippy finds SNPs between a haploid reference genome and your NGS sequence
reads. It will find both substitutions (snps) and insertions/deletions
(indels). It will use as many CPUs as you can give it on a single computer
(tested to 64 cores). It is designed with speed in mind, and produces a
consistent set of output files in a single folder. It can then take a set
of Snippy results using the same reference and generate a core SNP alignment
(and ultimately a phylogenomic tree).
NOTE
Since snippy 4.6.0 we had to update to a conda environment to facilitate use
of the new perl requirement.
Therefore, you’ll have to update your pipelines with the lines below, rather
than using the snippy from /local/cluster/bin.
To activate:
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bash
source /local/cluster/snippy/activate.sh
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Location and version:
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$ which snippy
/local/cluster/snippy-4.6.0/bin/snippy
$ snippy --version
snippy 4.6.0
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Version checks:
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$ snippy --check
[15:38:08] This is snippy 4.6.0
[15:38:08] Written by Torsten Seemann
[15:38:08] Obtained from https://github.com/tseemann/snippy
[15:38:08] Detected operating system: linux
[15:38:08] Enabling bundled linux tools.
[15:38:08] Found bwa - /local/cluster/snippy-4.6.0/bin/bwa
[15:38:08] Found bcftools - /local/cluster/snippy-4.6.0/bin/bcftools
[15:38:08] Found samtools - /local/cluster/snippy-4.6.0/bin/samtools
[15:38:08] Found java - /local/cluster/snippy-4.6.0/bin/java
[15:38:08] Found snpEff - /local/cluster/snippy-4.6.0/bin/snpEff
[15:38:08] Found samclip - /local/cluster/snippy-4.6.0/bin/samclip
[15:38:08] Found seqtk - /local/cluster/snippy-4.6.0/bin/seqtk
[15:38:08] Found parallel - /local/cluster/snippy-4.6.0/bin/parallel
[15:38:08] Found freebayes - /local/cluster/snippy-4.6.0/bin/freebayes
[15:38:08] Found freebayes-parallel - /local/cluster/snippy-4.6.0/bin/freebayes-parallel
[15:38:08] Found fasta_generate_regions.py - /local/cluster/snippy-4.6.0/bin/fasta_generate_regions.py
[15:38:08] Found vcfstreamsort - /local/cluster/snippy-4.6.0/bin/vcfstreamsort
[15:38:08] Found vcfuniq - /local/cluster/snippy-4.6.0/bin/vcfuniq
[15:38:08] Found vcffirstheader - /local/cluster/snippy-4.6.0/bin/vcffirstheader
[15:38:08] Found gzip - /bin/gzip
[15:38:08] Found vt - /local/cluster/snippy-4.6.0/bin/vt
[15:38:08] Found snippy-vcf_to_tab - /local/cluster/snippy-4.6.0/bin/snippy-vcf_to_tab
[15:38:08] Found snippy-vcf_report - /local/cluster/snippy-4.6.0/bin/snippy-vcf_report
[15:38:08] Checking version: samtools --version is >= 1.7 - ok, have 1.14
[15:38:08] Checking version: bcftools --version is >= 1.7 - ok, have 1.14
[15:38:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[15:38:09] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[15:38:09] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[15:38:09] Dependences look good!
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help message:
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$ snippy --help
SYNOPSIS
snippy 4.6.0 - fast bacterial variant calling from NGS reads
USAGE
snippy [options] --outdir <dir> --ref <ref> --R1 <R1.fq.gz> --R2 <R2.fq.gz>
snippy [options] --outdir <dir> --ref <ref> --ctgs <contigs.fa>
snippy [options] --outdir <dir> --ref <ref> --bam <reads.bam>
GENERAL
--help This help
--version Print version and exit
--citation Print citation for referencing snippy
--check Check dependences are installed then exit (default OFF)
--force Force overwrite of existing output folder (default OFF)
--quiet No screen output (default OFF)
RESOURCES
--cpus N Maximum number of CPU cores to use (default '8')
--ram N Try and keep RAM under this many GB (default '8')
--tmpdir F Fast temporary storage eg. local SSD (default '/data')
INPUT
--reference F Reference genome. Supports FASTA, GenBank, EMBL (not GFF) (default '')
--R1 F Reads, paired-end R1 (left) (default '')
--R2 F Reads, paired-end R2 (right) (default '')
--se F Single-end reads (default '')
--ctgs F Don't have reads use these contigs (default '')
--peil F Reads, paired-end R1/R2 interleaved (default '')
--bam F Use this BAM file instead of aligning reads (default '')
--targets F Only call SNPs from this BED file (default '')
--subsample n.n Subsample FASTQ to this proportion (default '1')
OUTPUT
--outdir F Output folder (default '')
--prefix F Prefix for output files (default 'snps')
--report Produce report with visual alignment per variant (default OFF)
--cleanup Remove most files not needed for snippy-core (inc. BAMs!) (default OFF)
--rgid F Use this @RG ID: in the BAM header (default '')
--unmapped Keep unmapped reads in BAM and write FASTQ (default OFF)
PARAMETERS
--mapqual N Minimum read mapping quality to consider (default '60')
--basequal N Minimum base quality to consider (default '13')
--mincov N Minimum site depth to for calling alleles (default '10')
--minfrac n.n Minumum proportion for variant evidence (0=AUTO) (default '0')
--minqual n.n Minumum QUALITY in VCF column 6 (default '100')
--maxsoft N Maximum soft clipping to allow (default '10')
--bwaopt F Extra BWA MEM options, eg. -x pacbio (default '')
--fbopt F Extra Freebayes options, eg. --theta 1E-6 --read-snp-limit 2 (default '')
SOURCE
https://github.com/tseemann/snippy - Torsten Seemann
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software ref: https://github.com/tseemann/snippy
research ref: <>