Mercurial > repos > stef > falco
diff falco-call.sh @ 26:0220bfeefbc1 draft
Uploaded
| author | stef |
|---|---|
| date | Fri, 10 Oct 2014 06:16:19 -0400 |
| parents | 2210b89487c6 |
| children | bff3cf6954f7 |
line wrap: on
line diff
--- a/falco-call.sh Fri Oct 10 06:13:06 2014 -0400 +++ b/falco-call.sh Fri Oct 10 06:16:19 2014 -0400 @@ -62,10 +62,14 @@ source $init_file -echo "--- sam ---" +echo "------ --- ------" +echo "------ sam ------" +echo "------ --- ------" samtools -#echo "--- bcf ---" -#bcftools +echo "------ --- ------" +echo "------ sam ------" +echo "------ --- ------" +bcftools #echo "--- snpsift ---" #java -jar $snpSift/SnpSift.jar #echo "--- snpeff ---" @@ -73,13 +77,14 @@ #echo "--- varscan ---" #java -jar $varScan -exit 0 +## DEBUG +#exit 0 ## ---------- ## create output files dir ## ---------- -mkdir $out_path -mkdir $out_path/$bam_base +#mkdir $out_path +#mkdir $out_path/$bam_base ## ---------- ## running analysis