File: vcfgtcompare.sh

package info (click to toggle)
libvcflib 1.0.12%2Bdfsg-1
  • links: PTS, VCS
  • area: main
  • in suites: sid, trixie
  • size: 70,520 kB
  • sloc: cpp: 39,837; python: 532; perl: 474; ansic: 317; ruby: 295; sh: 254; lisp: 148; makefile: 123; javascript: 94
file content (17 lines) | stat: -rwxr-xr-x 414 bytes parent folder | download | duplicates (3) 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
 
#!/bin/bash
# annotates records in the first file with genotypes and sites from the second
#
if [ $# != 3 ];
then
    echo "usage: $0 [annotation] [fileA] [fileB]"
    echo "annotates records in the first file with genotypes and sites from the second"
    exit
fi

annotation=$1
fileA=$2
fileB=$3

vcfcommonsamples $fileA $fileB \
 | vcfannotategenotypes $annotation - $fileB \
 | vcfgenotypecompare $annotation -