You need to tell the shell what a variable to be substituted is, since in this case it doesn't know were it stops being a variable.
This, for the shell means:
Code:
$id_$panel_$OMR_Filtered.vcf
substitute variable $id_
substitute variable $panel_
substitute variable $OMR_Filtered
Since those variables do not exist it will accept null, leaving only .vcf, which does not exist.
Hey guys, need some help. Running AIX Version 5.2 and one of our cron jobs is writing errors to a log file. Any ideas on the following error message.
Error: Internal system error: Unable to initialize standard output file
I'm guessing more info might be needed, so let me know.
Thanks (2 Replies)
hi there
i write one awk script file in shell programing
the code is related to dd/mm/yy to month, day year format
but i get an error
please can anybody help me out in this problem ??????
i give my code here including error
awk `
# date-month -- convert mm/dd/yy to month day,... (2 Replies)
I encounters a VSIFAX related error:
vfxstat: Cannot login to server on rsac3: Connect error to host 172.16.1.45: Invalid argument
It started happening last night with a core dump. Then we can't start VSIFAX again.
I am runing VSI-FAX 4.2 on AIX box (0 Replies)
--------------------------------------------------------------------------------
Hello, help me please.
I am trying to create a mksysb bakup using nim. I am geting this error, how to correct it ? :
Command : failed stdout: yes stderr: no... (9 Replies)
Hi Guys.
This is part of my filesystem structure :
Filesystem size used avail capacity Mounted on
/dev/md/dsk/d0 47G 5.2G 42G 12% /
/devices 0K 0K 0K 0% /devices
ctfs 0K 0K 0K 0% ... (2 Replies)
Hi - I am getting the error
`Error reading response length from authentication socket'
when I ssh from my cluster to another cluster, and then back to my cluster. It doesn't seem to affect anything, but it's just annoying that it always pops up and tends to confuse new users of the cluster. I... (1 Reply)
im kinda new to shell scripting so i need some help
i try to run this script and get the error code
> 5 ")syntax error: operand expected (error token is "
the code for the script is
#!/bin/sh
#
# script to see if the given value is correct
#
# Define errors
ER_AF=86 # Var is... (4 Replies)
what is this error log = hda: irq timeout: error=0x00 and how to solve?
every day upon checking the logs i see this error.
hda: irq timeout: error=0x00
hda: irq timeout: error=0x00
hda: irq timeout: error=0x00
hda: irq timeout: error=0x00
hw_client: segfault at 0000000000000046 rip... (3 Replies)
I have two servers with a fresh install of Solaris 11, and having problems when doing rpcinfo between them. There is no firewall involved, so everything should theoretically be getting through. Does anyone have any ideas? I did a lot of Google searches, and haven't found a working solution yet.
... (2 Replies)
I am writing a shell script with 2 run time arguments. During the execution if i got any error, then it needs to redirected to a error file and in console. Also both error and output to be redirected to a log file. But i am facing the below error.
#! /bin/sh
errExit ()
{
errMsg=`cat... (1 Reply)
Discussion started by: sarathy_a35
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)