Mercurial > repos > stef > falco
diff falco-call.sh @ 59:73eda23fb8fd draft
Uploaded
| author | stef |
|---|---|
| date | Wed, 25 Feb 2015 08:50:56 -0500 |
| parents | e7de191375e6 |
| children |
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--- a/falco-call.sh Thu Jan 08 06:18:04 2015 -0500 +++ b/falco-call.sh Wed Feb 25 08:50:56 2015 -0500 @@ -65,6 +65,8 @@ ## running analysis ## ---------- echo "[INFO] Starting variant calling" +## NOTE: if $FILTER_PARAM is set it includes the param name (--filter) +## NOTE: if $MANIFEST_PARAM is set it includes the param name (--manifest) CALL_STRING="$TOOLDIR/falco/bin/falco --bam $bam_file --output $bam_base --ref $REF_FILE $FILTER_PARAM $MANIFEST_PARAM" echo "[INFO] "$CALL_STRING perl $CALL_STRING @@ -105,6 +107,9 @@ #cp 'index.html' $html_out # this is the overview of samples html #cp $bam_base'.html' $out_path/'out.html' # this is the sample html cp $bam_base'.falco.vcf' $vcf_out +cp $bam_base'.qc.ann.qual.txt' $qc_ann_qual_out +cp $bam_base'.qc2.ann.txt' $qc2_ann_txt_out +cp $bam_base'.qc.targets.txt' $qc_targets_txt_out ## ---------- ## copy files to keep to output path