adding checkmate bash script

variants/checkmate.sh

+#!/bin/bash
+#checkmate.sh
+
+usage() {
+  echo "-h Help documentation for checkmate"
+  echo "-r  --Path to Reference Genome with the file genome.fa"
+  echo "-p  --Prefix for output file name"
+  echo "-c  --Path to Reference GenomeNGS Checkmate SNP BED file"
+  echo "Example: bash checkmate.sh -p prefix -r /path/GRCh38 -c /path/NGSCheckMate.bed -f"
+  exit 1
+}
+
+OPTIND=1 # Reset OPTIND
+while getopts :r:l:n:c:b:p:fh opt
+do
+    case $opt in
+        r) index_path=$OPTARG;;
+        p) pair_id=$OPTARG;;
+        b) sbam=$OPTARG;;
+        n) normal=$OPTARG;;
+	f) filter=1;;
+	c) capture=$OPTARG;;
+        h) usage;;
+    esac
+done
+function join_by { local IFS="$1"; shift; echo "$*"; }
+
+shift $(($OPTIND -1))
+baseDir="`dirname \"$0\"`"
+
+# Check for mandatory options
+source /etc/profile.d/modules.sh	
+export PATH=/project/shared/bicf_workflow_ref/seqprg/bin:/usr/local/bin/:$PATH
+
+module load samtools/gcc/1.8 bcftools/gcc/1.8
+
+if [[ -z $capture ]]
+then
+    capture="${index_path}/NGSCheckMate.bed"
+fi
+
+if [[ -f "${index_path}/genome.fa" ]]
+then
+    reffa="${index_path}/genome.fa"
+fi
+
+for i in *.bam; do
+    prefix="${i%.bam}"
+    echo ${prefix}
+    bcftools mpileup -A -d 1000000 -C50 -Ou --gvcf 0 -f ${reffa} -T ${capture} $i | bcftools call -m --gvcf 0 -Ov | bcftools convert --gvcf2vcf -f ${reffa} -Ov -o ${prefix}.vcf
+done
+
+if [[ -f /project/shared/bicf_workflow_ref/seqprg/bin/ncm.py ]]
+then
+    ncm=/project/shared/bicf_workflow_ref/seqprg/bin/ncm.py
+elif [[ -f /usr/local/bin/ncm.py ]]
+then
+    ncm=/usr/local/bin/ncm.py
+else
+    echo "ncm missing"
+fi
+
+python $ncm -V -d ./ -bed $capture -O ./ -N ${pair_id}
+perl $baseDir/sequenceqc_somatic.pl -i ${pair_id}_all.txt -o ${pair_id}.sequence.stats.txt

variants/sequenceqc_somatic.pl

+#!/usr/bin/perl -w
+#uploadqc.pl
+
+use Getopt::Long qw(:config no_ignore_case no_auto_abbrev);
+my %opt = ();
+my $results = GetOptions (\%opt,'input|i=s','output|o=s','help|h');
+
+open MATE, "<$opt{input}" or die $!;
+
+while (my $line = <MATE>) {
+    chomp($line);
+    my ($sam1,$pf,$sam2,$corr,$depth) = split(/\t/,$line);
+    $sam1 = (split(/\./,$sam1))[0];
+    $sam2 = (split(/\./,$sam2))[0];
+    open OUT, ">$opt{output}" or die $!;
+    my $status= 'PASS';	
+    $status='FAIL' if($pf eq 'unmatched');
+    print OUT join("\n","Sample_1\t".$sam1,"Sample_2\t".$sam2,"Correlation\t".$corr,
+		   "Depth\t".$depth,"Status\t".$status),"\n";
+}