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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified April 30, 2019
Description: Filters VCF files by position or other attributes.
Filtering by optional fields (such as allele frequency) require VCF files
generated by CallVariants.
Usage: filtervcf.sh in=<file> out=<file>
I/O parameters:
in=<file> Input VCF.
out=<file> Output VCF.
ref=<file> Reference fasta (optional).
overwrite=f (ow) Set to false to force the program to abort rather than
overwrite an existing file.
bgzip=f Use bgzip for gzip compression.
splitalleles=f Split multi-allelic lines into multiple lines.
splitsubs=f Split multi-base substitutions into SNPs.
canonize=t Trim variations down to a canonical representation.
Position-filtering parameters:
minpos= Ignore variants not overlapping this range.
maxpos= Ignore variants not overlapping this range.
contigs= Comma-delimited list of contig names to include. These
should have no spaces, or underscores instead of spaces.
invert=f Invert position filters.
Type-filtering parameters:
sub=t Keep substitutions.
del=t Keep deletions.
ins=t Keep insertions.
Variant-quality filtering parameters:
minreads=0 Ignore variants seen in fewer reads.
minqualitymax=0 Ignore variants with lower max base quality.
minedistmax=0 Ignore variants with lower max distance from read ends.
minmapqmax=0 Ignore variants with lower max mapq.
minidmax=0 Ignore variants with lower max read identity.
minpairingrate=0.0 Ignore variants with lower pairing rate.
minstrandratio=0.0 Ignore variants with lower plus/minus strand ratio.
minquality=0.0 Ignore variants with lower average base quality.
minedist=0.0 Ignore variants with lower average distance from ends.
minavgmapq=0.0 Ignore variants with lower average mapq.
minallelefraction=0.0 Ignore variants with lower allele fraction. This
should be adjusted for high ploidies.
minid=0 Ignore variants with lower average read identity.
minscore=0.0 Ignore variants with lower Phred-scaled score.
clearfilters Reset all variant filters to zero.
There are additionally max filters for score, quality, mapq, allelefraction,
and identity.
Java Parameters:
-Xmx This will set Java's memory usage, overriding autodetection.
-Xmx20g will specify 20 gigs of RAM, and -Xmx200m will
specify 200 megs. The max is typically 85% of physical memory.
-eoom This flag will cause the process to exit if an out-of-memory
exception occurs. Requires Java 8u92+.
-da Disable assertions.
Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
"
}
#This block allows symlinked shellscripts to correctly set classpath.
pushd . > /dev/null
DIR="${BASH_SOURCE[0]}"
while [ -h "$DIR" ]; do
cd "$(dirname "$DIR")"
DIR="$(readlink "$(basename "$DIR")")"
done
cd "$(dirname "$DIR")"
DIR="$(pwd)/"
popd > /dev/null
#DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
CP="$DIR""current/"
z="-Xmx4g"
z2="-Xms4g"
set=0
if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
usage
exit
fi
calcXmx () {
source "$DIR""/calcmem.sh"
setEnvironment
parseXmx "$@"
if [[ $set == 1 ]]; then
return
fi
freeRam 4000m 42
z="-Xmx${RAM}m"
z2="-Xms${RAM}m"
}
calcXmx "$@"
filtervcf() {
local CMD="java $EA $EOOM $z $z2 -cp $CP var2.FilterVCF $@"
echo $CMD >&2
eval $CMD
}
filtervcf "$@"
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