lofreq/lofreq_call

variant calling

low frequancy variant calling

lofreq

lofreq/call

Description

Call variants from a BAM file.

LoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or base/indel alignment uncertainty), which are usually ignored by other methods or only used for filtering.

LoFreq* can run on almost any type of aligned sequencing data (e.g. Illumina, IonTorrent or Pacbio) since no machine- or sequencing-technology dependent thresholds are used. It automatically adapts to changes in coverage and sequencing quality and can therefore be applied to a variety of data-sets e.g. viral/quasispecies, bacterial, metagenomics or somatic data.

LoFreq* is very sensitive; most notably, it is able to predict variants below the average base-call quality (i.e. sequencing error rate). Each variant call is assigned a p-value which allows for rigorous false positive control. Even though it uses no approximations or heuristics, it is very efficient due to several runtime optimizations and also provides a (pseudo-)parallel implementation. LoFreq* is generic and fast enough to be applied to high-coverage data and large genomes. On a single processor it takes a minute to analyze Dengue genome sequencing data with nearly 4000X coverage, roughly one hour to call SNVs on a 600X coverage E.coli genome and also roughly an hour to run on a 100X coverage human exome dataset.

Inputs

Name	Type & Properties	Description
--input	file required	Input BAM file.
--input_bai	file required	Index file for the input BAM file.
--ref -f	file required	Indexed reference fasta file (gzip supported). Default: none.

Name

Type & Properties

--input

file

required

--input_bai

file

required

--ref

-f

file

required

Outputs

Name	Type & Properties	Description
--out -o	file required output	Vcf output file. Default: stdout.

Name

Type & Properties

--out

-o

file

required

output

Arguments

Name	Type & Properties	Description
--region -r	string	Limit calls to this region (chrom:start-end). Default: none.
--bed -l	file	List of positions (chr pos) or regions (BED). Default: none.
--min_bq -q	integer	Skip any base with baseQ smaller than INT. Default: 6.
--min_alt_bq -Q	integer	Skip alternate bases with baseQ smaller than INT. Default: 6.
--def_alt_bq -R	integer	Overwrite baseQs of alternate bases (that passed bq filter) with this value (-1: use median ref-bq; 0: keep). Default: 0.
--min_jq -j	integer	Skip any base with joinedQ smaller than INT. Default: 0.
--min_alt_jq -J	integer	Skip alternate bases with joinedQ smaller than INT. Default: 0.
--def_alt_jq -K	integer	Overwrite joinedQs of alternate bases (that passed jq filter) with this value (-1: use median ref-bq; 0: keep). Default: 0.
--no_baq -B	boolean_true	Disable use of base-alignment quality (BAQ).
--no_idaq -A	boolean_true	Don't use IDAQ values (NOT recommended under ANY circumstances other than debugging).
--del_baq -D	boolean_true	Delete pre-existing BAQ values, i.e. compute even if already present in BAM.
--no_ext_baq -e	boolean_true	Use 'normal' BAQ (samtools default) instead of extended BAQ (both computed on the fly if not already present in lb tag).
--min_mq -m	integer	Skip reads with mapping quality smaller than INT. Default: 0.
--max_mq -M	integer	Cap mapping quality at INT. Default: 255.
--no_mq -N	boolean_true	Don't merge mapping quality in LoFreq's model.
--call_indels	boolean_true	Enable indel calls (note: preprocess your file to include indel alignment qualities!).
--only_indels	boolean_true	Only call indels; no SNVs.
--src_qual -s	boolean_true	Enable computation of source quality.
--ign_vcf -S	file	Ignore variants in this vcf file for source quality computation. Multiple files can be given separated by commas.
--def_nm_q -T	integer	If >= 0, then replace non-match base qualities with this default value. Default: -1.
--sig -a	double	P-Value cutoff / significance level. Default: 0.010000.
--bonf -b	string	Bonferroni factor. 'dynamic' (increase per actually performed test) or INT. Default: Dynamic.
--min_cov -C	integer	Test only positions having at least this coverage. Default: 1. (note: without --no-default-filter default filters (incl. coverage) kick in after predictions are done).
--max_depth -d	integer	Cap coverage at this depth. Default: 1000000.
--illumina_13	boolean_true	Assume the quality is Illumina-1.3-1.7/ASCII+64 encoded.
--use_orphan	boolean_true	Count anomalous read pairs (i.e. where mate is not aligned properly).
--plp_summary_only	boolean_true	No variant calling. Just output pileup summary per column.
--no_default_filter	boolean_true	Don't run default 'lofreq filter' automatically after calling variants.
--force_overwrite	boolean_true	Overwrite any existing output.
--verbose	boolean_true	Be verbose.
--debug	boolean_true	Enable debugging.

Name

Type & Properties

--region

-r

string

--bed

-l

file

--min_bq

-q

integer

--min_alt_bq

-Q

integer

--def_alt_bq

-R

integer

--min_jq

-j

integer

--min_alt_jq

-J

integer

--def_alt_jq

-K

integer

--no_baq

-B

boolean_true

--no_idaq

-A

boolean_true

--del_baq

-D

boolean_true

--no_ext_baq

-e

boolean_true

--min_mq

-m

integer

--max_mq

-M

integer

--no_mq

-N

boolean_true

--call_indels

boolean_true

--only_indels

boolean_true

--src_qual

-s

boolean_true

--ign_vcf

-S

file

--def_nm_q

-T

integer

--sig

-a

double

--bonf

-b

string

--min_cov

-C

integer

--max_depth

-d

integer

--illumina_13

boolean_true

--use_orphan

boolean_true

--plp_summary_only

boolean_true

--no_default_filter

boolean_true

--force_overwrite

boolean_true

--verbose

boolean_true

--debug

boolean_true

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
out: "$id.$key.out.vcf"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.1.0 \  
  -main-script target/nextflow/lofreq/lofreq_call/main.nf \  
  -params-file params.yaml

lofreq/lofreq_call

Inputs

Outputs

Arguments

Run this component

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