NGS Illumina pipeline main caller

#!/usr/bin/perl
use lib './';
use NGS_Illumina;


# Assume the paths for fastx_tk, maq, bwa, samtools are in ENV{PATH}; check $PATH setting $HOME/.bash_profile
# Assume perl and python are installed
my $NGS_obj = new NGS_Illumina ('sample_name' => 'Testis_T28',
'input_fq1' => 'Run1_testicular-28T_lane2_read1_sequence.txt',
'input_fq2' => 'Run1_testicular-28T_lane2_read2_sequence.txt',
'pe' => 1,
'reference_fa' => '/data/public/reference_genomes/genome_hg18.fa',
'dbsnp_rod' => '/data/nextgen1/pipeline/dbsnp_130_hg18.rod',
'target_bed' => '/data/nextgen1/pipeline/targets/SureSelect_All_Exon_G3362_with_names.v2.bed', #Agilent SureSelect Target Enrichment
'picard_dir' => '/home/gmslz/tools/picard-tools-1.44',
'gatk_dir' => '/data/public/tools/gatk-v4333/Sting',
'tmp_dir' => '/home/tmp',
'java_mem' => '-Xmx4g');

$NGS_obj -> check_fastq_format();
#$NGS_obj -> illumina2sanger();
#$NGS_obj -> qcstats();
#$NGS_obj -> fastq_trimmer(1, 74);
#$NGS_obj -> aln_bwa(); #alignment step, which includes bwa, sort, rm_pcrdup, add_rg
$NGS_obj -> snp_analysis_gatk(); #gatk step, which includes realignment, recalibration, genotyping (indel, snp)