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Command.GATK3.8.pl
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#! perl
use warnings;
use strict;
use File::Basename;
use Cwd qw(abs_path getcwd);
use Getopt::Long;
if(!$ARGV[0]){
print STDERR "USAGE : perl $0 [realign|snpcall|fixsnp]\n";
exit;
}
if ($ARGV[0] eq "realign"){
&realign();
}
if ($ARGV[0] eq "snpcall"){
&snpcall();
}
if ($ARGV[0] eq "fixsnp"){
&fixsnp();
}
sub fixsnp{
my $gatk = "/data/00/user/user112/software/gatk3.8-1/GenomeAnalysisTK.jar";
my $pl = "/data/00/user/user112/code/script/GATK.remove.hdfilter.pl";
my($ref,@in_dir,$out_dir,$threads,$cover);
GetOptions(
'ref=s' => \$ref,
'in=s' => \@in_dir,
'out=s' => \$out_dir,
'cover' => \$cover,
);
if ((! $ref) || (scalar @in_dir == 0)){
&print_help2;
exit;
}
$out_dir //= ".";
mkdir $out_dir if !-e $out_dir;
open O,'>',"0.downstream.sh";
my @files;
for my $dir (@in_dir){
my @t_file = sort{$a cmp $b} grep {/.*gvcf.gz$/} `find $dir`;
push @files , @t_file;
}
print O "java -jar $gatk -T GenotypeGVCFs -R $ref";
map{chomp($_);print O " -V ./$_"} @files;
print O " -o $out_dir/Pop.vcf.gz\n";
print O "java -jar $gatk -T SelectVariants -R $ref -V $out_dir/Pop.vcf.gz -selectType SNP -o $out_dir/Pop.SNP.vcf.gz\n";
print O "java -jar $gatk -T SelectVariants -R $ref -V $out_dir/Pop.vcf.gz -selectType INDEL -o $out_dir/Pop.INDEL.vcf.gz\n";
print O "java -jar $gatk -T VariantFiltration -R $ref -V $out_dir/Pop.SNP.vcf.gz --filterExpression \"QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0\" --filterName \"my_snp_filter\" -o $out_dir/Pop.HDflt.SNP.vcf.gz
java -jar $gatk -T VariantFiltration -R $ref -V $out_dir/Pop.INDEL.vcf.gz --filterExpression \"QD < 2.0 || FS > 200.0 || ReadPosRankSum < -20.0\" --filterName \"my_indel_filter\" -o $out_dir/Pop.HDflt.INDEL.vcf.gz
perl $pl --input $out_dir/Pop.HDflt.SNP.vcf.gz --out $out_dir/Pop.HDflted.SNP.vcf.gz --type SNP --marker my_snp_filter --multi
perl $pl --input $out_dir/Pop.HDflt.INDEL.vcf.gz --out $out_dir/Pop.HDflted.INDEL.vcf.gz --type INDEL --marker my_indel_filter\n"
}
sub snpcall{
my $gatk = "/data/00/user/user112/software/gatk3.8-1/GenomeAnalysisTK.jar";
my($ref,@in_dir,$out_dir,$threads,$cover);
GetOptions(
'ref=s' => \$ref,
'in=s' => \@in_dir,
'out=s' => \$out_dir,
'threads=s' => \$threads,
'cover' => \$cover,
);
if ((! $ref) || (scalar @in_dir == 0)){
&print_help1;
exit;
}
$out_dir //= ".";
$threads //= 10;
mkdir $out_dir if !-e $out_dir;
my @check = grep{/tbi$/}`find $out_dir`;
my %c;
for(@check){
chomp;
(my $n = basename $_) =~ s/.gvcf.gz.tbi.*//;
$c{$n} = 1;
}
my @files;
for my $dir (@in_dir){
my @t_file = sort{$a cmp $b} grep {/.*bam$/} `find $dir`;
push @files , @t_file;
}
open O,'>',"0.HaploteCaller.sh";
foreach (@files) {
chomp;
my $dir = dirname $_;
(my $o_name = basename $_) =~ s/(.*?)\..*/$1/;
(my $bam_index = basename $_) =~ s/\.bam$/\.bai/;
next if !-e "$dir/$bam_index";
if(!$cover){
next if exists $c{$o_name};
}
print O "java -jar $gatk -T HaplotypeCaller -R $ref -I $_ -nct $threads -ERC GVCF -o $out_dir/$o_name.gvcf.gz -variant_index_type LINEAR -variant_index_parameter 128000 --min_mapping_quality_score 20 2>>$out_dir/$o_name.log\n";
#print "gatk --java-options \"-Xmx20g\" -R $ref -I $_ -O $o_name.g.vcf.gz --emit-ref-confidence GVCF\n";
}
close O;
}
sub realign{
my $gatk = "/data/00/user/user112/software/gatk3.8-1/GenomeAnalysisTK.jar";
my($ref,@in_dir,$out_dir,$threads,$cover);
GetOptions(
'ref=s' => \$ref,
'in=s' => \@in_dir,
'out=s' => \$out_dir,
'threads=s' => \$threads,
'cover' => \$cover,
);
if ((! $ref) || (scalar @in_dir == 0)){
&print_help1;
exit;
}
$out_dir //= ".";
$threads //= 10;
mkdir $out_dir if !-e $out_dir;
my @files;
for my $dir (@in_dir){
my @t_file = sort{$a cmp $b} grep {/.*nodup.bam$/} `find $dir`;
push @files , @t_file;
}
open O1,'>',"0.Realigner1.sh";
open O2,'>',"0.Realigner2.sh";
foreach (@files) {
chomp;
(my $o_name = basename $_) =~ s/(.*?)\..*/$1/;
next if -s "$out_dir/$o_name.realn.bam";
print O2 "java -jar $gatk -T IndelRealigner -R $ref -targetIntervals $out_dir/$o_name.realn.intervals -o $out_dir/$o_name.realn.bam -I $_ 2>$out_dir/$o_name.realn.bam.log\n";
next if -s "$out_dir/$o_name.realn.intervals";
print O1 "java -jar $gatk -T RealignerTargetCreator -nt $threads -R $ref -I $_ -o $out_dir/$o_name.realn.intervals 2>$out_dir/$o_name.TC.bam.log\n";
}
close O1;
close O2;
}
sub print_help1{
print STDERR"
Usage: perl GATK3.8.pl realign|snpcall --in <bam dir> --ref <path2genome>
--ref genome ref_file , with samtools fai and picard dict file
--in dir contain bam file
Options:
--out defalut [./]
--threads defalut [10]
--cover
";
}
sub print_help2{
print STDERR"
Usage: perl GATK3.8.pl realign|snpcall --in <bam dir> --ref <path2genome>
--ref genome ref_file , with samtools fai and picard dict file
--in dir contain g.vcf file
Options:
--out defalut [./]
--threads defalut [10]
";
}