Mercurial > repos > ulfschaefer > phephenix

annotate filter_vcf.sh @ 11:dcb9cd1ade0a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author ulfschaefer
date Fri, 29 Apr 2016 07:19:52 -0400
parents 45ff0fc972e8
children a6079f6217f5
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
45ff0fc972e8 Uploaded
ulfschaefer
parents:
diff changeset
1 #!/bin/bash
45ff0fc972e8 Uploaded
ulfschaefer
parents:
diff changeset
2
45ff0fc972e8 Uploaded
ulfschaefer
parents:
diff changeset
3 echo $@
45ff0fc972e8 Uploaded
ulfschaefer
parents:
diff changeset
4
45ff0fc972e8 Uploaded
ulfschaefer
parents:
diff changeset
5 OUTPUT=$1
45ff0fc972e8 Uploaded
ulfschaefer
parents:
diff changeset
6 shift
45ff0fc972e8 Uploaded
ulfschaefer
parents:
diff changeset
7 VCF=$1
45ff0fc972e8 Uploaded
ulfschaefer
parents:
diff changeset
8 shift
45ff0fc972e8 Uploaded
ulfschaefer
parents:
diff changeset
9 FILTERS=$@
45ff0fc972e8 Uploaded
ulfschaefer
parents:
diff changeset
10
45ff0fc972e8 Uploaded
ulfschaefer
parents:
diff changeset
11 FILTERS=$(echo -n $FILTERS | sed 's/ /,/g')
45ff0fc972e8 Uploaded
ulfschaefer
parents:
diff changeset
12
45ff0fc972e8 Uploaded
ulfschaefer
parents:
diff changeset
13 CMD="phenix.py filter_vcf --vcf $VCF --filters $FILTERS --output $OUTPUT"
45ff0fc972e8 Uploaded
ulfschaefer
parents:
diff changeset
14
45ff0fc972e8 Uploaded
ulfschaefer
parents:
diff changeset
15 echo "CMD: "$CMD
45ff0fc972e8 Uploaded
ulfschaefer
parents:
diff changeset
16 eval $CMD