As an exercise, I'm trying to re-write this code without the compound square brackets, using grep and test. Need to know what to do about the "equal-tilde".
Okay, well this is more or less my first attempt at writing a shell script.
Anyways, here's my code:
cd ${PATH}
if
then
rm ${FILE}
./anotherScript
else
exit 1
fi
exit 1
Anyways, it's a pretty simple script that is supposed to search for the... (4 Replies)
Hello, i have a script which checks if the user entered 8 numeric characters in the form of YYYYMMDD (birth date). If the user entered any non numeric characters, an error will be displayed:
# Check to see if the 8 characters are all numbers
# If not show error essage
# And prompt user... (4 Replies)
Hi,
I want to use grep inside a test statement, but I am getting an error message.
Two variables
testvarNum=5
testvarNonNum=x
echo $testvarNum | grep *
The result of this is as follows:
5
However, when I try the following (i.e. to test if the variable is numeric or non-numeric):... (3 Replies)
This is the code:
while test 1 -eq 1
do
read a
$a
if test $a = stop
then
break
fi
done
I read a command on every loop an execute it.
I check if the string equals the word stop to end the loop,but it say that I gave too many arguments to test.
For example echo hello.
Now the... (1 Reply)
Hello ...again.
I am stuck on this part, I have a loop with processes an operations file.
and calls different functions depending on what is in loop, which processes a database file...
#so far my add function works as intended
add()
{
...blah blah;
}
# delete is kinda working... (13 Replies)
Hello,
I have a problem. I will search files on fileextentions (suffix). It can with the command find, but I will do it with the commands grep and/or test. When i start the script I will see all files with that extention (suffix).
Can anyone help me, please?
Thanks!
Regards,
Arjan... (4 Replies)
Hi all. I am trying to compare and filter two files. I have a bigfile.txt of names and ids and a smallfile.txt of ids only. What I am trying to do is use a while read loop to read the ids in the bigfile and then echo the name and id only if the id exists in the small file. Basically, I'm trying to... (5 Replies)
read a
if test grep EOF $a
then echo yes file
else
echo no
fi (1 Reply)
Discussion started by: iamsumibisht
1 Replies
LEARN ABOUT DEBIAN
vcf-annotate
VCF-ANNOTATE(1) User Commands VCF-ANNOTATE(1)NAME
vcf-annotate - annotate VCF file, add filters or custom annotations
SYNOPSIS
cat in.vcf | vcf-annotate [OPTIONS] > out.vcf
DESCRIPTION
About: Annotates VCF file, adding filters or custom annotations. Requires tabix indexed file with annotations.
Currently annotates only the INFO column, but it will be extended on demand.
OPTIONS -a, --annotations <file.gz>
The tabix indexed file with the annotations: CHR FROM[ TO][ VALUE]+.
-c, --columns <list>
The list of columns in the annotation file, e.g. CHROM,FROM,TO,-,INFO/STR,INFO/GN. The dash in this example indicates that the third
column should be ignored. If TO is not present, it is assumed that TO equals to FROM.
-d, --description <file|string>
Header annotation, e.g. key=INFO,ID=HM2,Number=0,Type=Flag,Description='HapMap2 membership'. The descriptions can be read from a
file, one annotation per line.
-f, --filter <list>
Apply filters, list is in the format flt1=value/flt2/flt3=value/etc.
-h, -?, --help
This help message.
Filters:
+ Apply all filters with default values (can be overridden, see the example below).
-X Exclude the filter X
1, StrandBias
FLOAT Min P-value for strand bias (given PV4) [0.0001]
2, BaseQualBias
FLOAT Min P-value for baseQ bias [1e-100]
3, MapQualBias
FLOAT Min P-value for mapQ bias [0]
4, EndDistBias
FLOAT Min P-value for end distance bias [0.0001]
a, MinAB
INT Minimum number of alternate bases [2]
c, SnpCluster
INT1,INT2 Filters clusters of 'INT1' or more SNPs within a run of 'INT2' bases []
D, MaxDP
INT Maximum read depth [10000000]
d, MinDP
INT Minimum read depth [2]
q, MinMQ
INT Minimum RMS mapping quality for SNPs [10]
Q, Qual
INT Minimum value of the QUAL field [10]
r, RefN
Reference base is N []
W, GapWin
INT Window size for filtering adjacent gaps [10]
w, SnpGap
INT SNP within INT bp around a gap to be filtered [10]
Example:
zcat in.vcf.gz | vcf-annotate -a annotations.gz -d descriptions.txt | bgzip -c >out.vcf.gz zcat in.vcf.gz | vcf-annotate -f
+/-a/c=3,10/q=3/d=5/-D -a annotations.gz -d descriptions.txt | bgzip -c >out.vcf.gz
Where descriptions.txt contains:
key=INFO,ID=GN,Number=1,Type=String,Description='Gene Name' key=INFO,ID=STR,Number=1,Type=Integer,Description='Strand'
vcf-annotate 0.1.5 July 2011 VCF-ANNOTATE(1)