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comparison falco-call.sh @ 59:73eda23fb8fd draft

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author stef
date Wed, 25 Feb 2015 08:50:56 -0500
parents e7de191375e6
children
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58:e7de191375e6 59:73eda23fb8fd
63 63
64 ## ---------- 64 ## ----------
65 ## running analysis 65 ## running analysis
66 ## ---------- 66 ## ----------
67 echo "[INFO] Starting variant calling" 67 echo "[INFO] Starting variant calling"
68 ## NOTE: if $FILTER_PARAM is set it includes the param name (--filter)
69 ## NOTE: if $MANIFEST_PARAM is set it includes the param name (--manifest)
68 CALL_STRING="$TOOLDIR/falco/bin/falco --bam $bam_file --output $bam_base --ref $REF_FILE $FILTER_PARAM $MANIFEST_PARAM" 70 CALL_STRING="$TOOLDIR/falco/bin/falco --bam $bam_file --output $bam_base --ref $REF_FILE $FILTER_PARAM $MANIFEST_PARAM"
69 echo "[INFO] "$CALL_STRING 71 echo "[INFO] "$CALL_STRING
70 perl $CALL_STRING 72 perl $CALL_STRING
71 echo "[INFO] done with variant calling" 73 echo "[INFO] done with variant calling"
72 74
103 ## creating galaxy history outputs 105 ## creating galaxy history outputs
104 ## ---------- 106 ## ----------
105 #cp 'index.html' $html_out # this is the overview of samples html 107 #cp 'index.html' $html_out # this is the overview of samples html
106 #cp $bam_base'.html' $out_path/'out.html' # this is the sample html 108 #cp $bam_base'.html' $out_path/'out.html' # this is the sample html
107 cp $bam_base'.falco.vcf' $vcf_out 109 cp $bam_base'.falco.vcf' $vcf_out
110 cp $bam_base'.qc.ann.qual.txt' $qc_ann_qual_out
111 cp $bam_base'.qc2.ann.txt' $qc2_ann_txt_out
112 cp $bam_base'.qc.targets.txt' $qc_targets_txt_out
108 113
109 ## ---------- 114 ## ----------
110 ## copy files to keep to output path 115 ## copy files to keep to output path
111 ## ---------- 116 ## ----------
112 #cp -r ./$bam_base/*png $out_path/$bam_base/ 117 #cp -r ./$bam_base/*png $out_path/$bam_base/