diff --git a/variants/somatic_vc.sh b/variants/somatic_vc.sh index 585d670425a5f345268dc43b4080984705fe5510..1e90c8667b62bc1b8dfb9ee0fb9e23df83227854 100644 --- a/variants/somatic_vc.sh +++ b/variants/somatic_vc.sh @@ -8,23 +8,25 @@ usage(){ echo "-r --Path to Reference Genome with the file genome.fa" echo "-n --Normal" echo "-t --Tumor" + echo "-p -- PairID" echo "-x --NormalID" echo "-y --TumorID" echo "-i --NormalBAM used for Mantra in the case of UMI consensus" echo "-j --TumorBAM used for Mantra in the case of UMI consensus" echo "-b --TargetBed" - echo "Example: bash somatic_vc.sh -a strelka2 -y ORD1_N_panel1385 -y ORD1_T_panel138 -n ORD1_N_panel1385.final.bam -t ORD1_T_panel1385.final.bam" + echo "Example: bash somatic_vc.sh -a strelka2 -p subj1 -y ORD1_N_panel1385 -y ORD1_T_panel138 -n ORD1_N_panel1385.final.bam -t ORD1_T_panel1385.final.bam" exit 1 } OPTIND=1 # Reset OPTIND -while getopts :n:t:r:x:y:i:j:a:b:h opt +while getopts :n:t:p:r:x:y:i:j:a:b:h opt do case $opt in r) index_path=$OPTARG;; x) tid=$OPTARG;; y) nid=$OPTARG;; + p) pair_id=$OPTARG;; n) normal=$OPTARG;; t) tumor=$OPTARG;; i) mnormal=$OPTARG;; @@ -46,7 +48,7 @@ if [[ -z $SLURM_CPUS_ON_NODE ]] then SLURM_CPUS_ON_NODE=1 fi -pair_id=${tid}_${nid} +#pair_id=${tid}_${nid} if [[ -z $mtumor ]] then mtumor=tumor diff --git a/variants/unionvcf.pl b/variants/unionvcf.pl index 5ca8f506d769216ed6061695a827bfe2746f5847..04b5572dffe84365e83a281c10d200a7300f976a 100755 --- a/variants/unionvcf.pl +++ b/variants/unionvcf.pl @@ -110,7 +110,7 @@ foreach $vcf (@vcffiles) { } my @callers = ('ssvar','sam','gatk','strelka2','platypus','hotspot'); if (grep(/mutect/,@vcffiles)) { - @callers = ('sssom','pmutect','shimmer','strelka2','varscan','virmid'); + @callers = ('sssom','mutect','shimmer','strelka2','varscan','virmid'); } F1:foreach $chr (sort {$a cmp $b} keys %lines) { F2:foreach $pos (sort {$a <=> $b} keys %{$lines{$chr}}) {