Merge pull request #15 from eipm/combine_pindels

Update combine_pindel_vcfs.sh
eipm · Dec 11, 2020 · 1104dae · 1104dae
2 parents 0cf9e41 + a7d1878
commit 1104dae
Showing 1 changed file with 1 addition and 5 deletions.
diff --git a/combine_pindel_vcfs.sh b/combine_pindel_vcfs.sh
@@ -1,5 +1 @@
-DOI=$1
-FOIS=( $(ls $DOI/*vcf | egrep -e '(pindel_LI|pindel_RP|pindel_SI|pindel_TD|pindel_INV|pindel_INT_final|pindel_D)') )
-FINAL_FILE=$DOI"/pindel_all.vcf"
-VCFS_STR=for i in "${FOIS[*]}"; do echo "$i"; done
-vcf-concat -p $VCFS_STR >  $FINAL_FILE
+vcf-concat -p $(ls ${1}/*vcf | egrep -e '(pindel_LI|pindel_RP|pindel_SI|pindel_TD|pindel_INV|pindel_INT_final|pindel_D)') > ${1}/pindel_all.vcf