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  1. 1. Usage
  2. 2. Details

1.  Usage

This pipeline exports variants in VCF format, call snpEff to predict its effect, and import the result as an variant info field EFF.

% vtools show pipeline snpEff
A pipeline to call snpEff to annotate variants.

Available pipelines: eff

Pipeline "eff":  This pipeline export variants in VCF format, call snpEff to
annotate it, and import the EFF info as an information field. This pipeline will
automatically download appropriate snpEff database (e.g. hg19).
  eff_0:              Load specified snapshot if a snapshot is specified. Otherwise
                      use the existing project.
  eff_10:             Check the existence of command java
  eff_11:             Check if snpEff is installed and executable
  eff_12:             Check the data storage location in snpEff.config file.
  eff_14:             Download reference database for the project reference genome
  eff_20:             Export variants in VCF format
  eff_30:             Execute snpEff eff to annotate variants
  eff_40:             Importing results from snpEff

Pipeline parameters:
  var_table           Variant table for the variants to be analyzed. (default:
                      variant)
  java                path to java. Default to 'java' (use $PATH to determine actual
                      path) (default: java)
  opt_java            Option to java program. -Djava.io.tmpdir is frequently used to
                      set java temporary directory if system temporary partition is
                      not big enough. (default: -Xmx4g -XX:-UseGCOverheadLimit)
  snpeff_path         Path to directory that contains snpEff.jar. (default: ./)
  eff_fields          Fields that will be imported to the project from the output of
                      snpEff. The default value is EFF, which is the whole EFF info.
                      You can also specify one or more off EFF_Type, EFF_Impact and
                      Eff_Functional_Class, which are from extracted from the
                      Effect(Effct_impact|Functional_Class... field. (default: EFF)

2.  Details

This pipeline calls snpEff to estimate the effect of variants so you first need to download and install snpEff.

% vtools execute snpEff eff --snpeff_path ~/bin/snpEff/
INFO: Executing step eff_0 of pipeline snpEff: Load specified snapshot if a snapshot is specified. Otherwise use the existing project.
INFO: Executing step eff_10 of pipeline snpEff: Check the existence of command java
INFO: Command java is located.
INFO: Executing step eff_11 of pipeline snpEff: Check if snpEff is installed and executable
INFO: Executing step eff_12 of pipeline snpEff: Check the data storage location in snpEff.config file.
INFO: Running cat /Users/bpeng/bin/snpEff//snpEff.config | grep "data_dir =" | cut -d= -f2 > cache/snpEff.data_dir
INFO: Command "cat /Users/bpeng/bin/snpEff//snpEff.config | grep "data_dir =" | cut -d= -f2 > cache/snpEff.data_dir" completed successfully in 00:00:01
INFO: Executing step eff_14 of pipeline snpEff: Download reference database for the project reference genome
INFO: Reuse existing files /Users/bpeng/snpEff/data//hg19/snpEffectPredictor.bin
INFO: Executing step eff_20 of pipeline snpEff: Export variants in VCF format
INFO: Running vtools export variant --format vcf --output cache/snpEff_input.vcf
INFO: Command "vtools export variant --format vcf --output cache/snpEff_input.vcf" completed successfully in 00:00:01
INFO: Executing step eff_30 of pipeline snpEff: Execute snpEff eff to annotate variants
INFO: Running java -jar /Users/bpeng/bin/snpEff//snpEff.jar -c /Users/bpeng/bin/snpEff//snpEff.config -v hg19 cache/snpEff_input.vcf > cache/snpEff_output.vcf
INFO: Command "java -jar /Users/bpeng/bin/snpEff//snpEff.jar -c /Users/bpeng/bin/snpEff//snpEff.config -v hg19 cache/snpEff_input.vcf > cache/snpEff_output.vcf" completed successfully in 00:00:34
INFO: Executing step eff_40 of pipeline snpEff: Importing results from snpEff
INFO: Running vtools update variant --from_file cache/snpEff_output.vcf --var_info EFF
INFO: Using primary reference genome hg19 of the project.
Getting existing variants: 100% [===========================================] 1,611 181.8K/s in 00:00:00
INFO: Updating variants from cache/snpEff_output.vcf (1/1)
snpEff_output.vcf: 100% [====================================================] 1,610 12.3K/s in 00:00:00
INFO: Field EFF of 1,611 variants are updated
INFO: Command "vtools update variant --from_file cache/snpEff_output.vcf --var_info EFF" completed successfully in 00:00:01

The field EFF is added to (or updated if it already exists) the project,

% vtools output variant chr pos ref alt EFF -l 10
6	32797167	A	G	INTRON(MODIFIER||||653|TAP2||CODING|NM_018833.2.8|11|1),INTRON(MODIFIER||||703|TAP2||CODING|NM_000544.3.8|11|1)
6	32369594	A	G	INTRON(MODIFIER||||455|BTNL2||CODING|NM_019602.1.8|3|1)
6	32797947	A	G	INTRON(MODIFIER||||653|TAP2||CODING|NM_018833.2.8|9|1),INTRON(MODIFIER||||703|TAP2||CODING|NM_000544.3.8|9|1)
6	32797168	A	G	INTRON(MODIFIER||||653|TAP2||CODING|NM_018833.2.8|11|1),INTRON(MODIFIER||||703|TAP2||CODING|NM_000544.3.8|11|1)
6	31380276	A	G	INTRON(MODIFIER||||332|MICA||CODING|NM_001177519.1.4|5|1),INTRON(MODIFIER||||383|MICA||CODING|NM_000247.1.5|6|1),INTRON(MODIFIER|||||MICA||CODING|NR_036523.1.5|5|1),INTRON(MODIFIER|||||MICA||CODING|NR_036524.1.4|5|1)
6	32369554	A	G	INTRON(MODIFIER||||455|BTNL2||CODING|NM_019602.1.8|4|1)
6	32369596	A	G	INTRON(MODIFIER||||455|BTNL2||CODING|NM_019602.1.8|3|1)
6	32369597	A	G	INTRON(MODIFIER||||455|BTNL2||CODING|NM_019602.1.8|3|1)
6	32369515	A	G	INTRON(MODIFIER||||455|BTNL2||CODING|NM_019602.1.8|4|1)
6	31380278	A	G	INTRON(MODIFIER||||332|MICA||CODING|NM_001177519.1.4|5|1),INTRON(MODIFIER||||383|MICA||CODING|NM_000247.1.5|6|1),INTRON(MODIFIER|||||MICA||CODING|NR_036523.1.5|5|1),INTRON(MODIFIER|||||MICA||CODING|NR_036524.1.4|5|1)