Do somebody have idea How to sort standard input without first line which in my case it's header
Example:
Cnt|VT |STAT|Date |Time |From |Alert Message |Instance |
125| | | 260308 |160026 |ZAMUAT2|ifpollq... (8 Replies)
Hello,
I have a header which I have to add to a sorted file, however if I use
cat header sortedfile > newfile, the operation takes 2 minutes as the sorted file is over 400mb.
I have noticed that when I sort the 400mb unsorted file, this only takes 14 seconds to create the output.
As... (2 Replies)
Hi,
I'm ssh'ing into a server using ruby and sending a one-liner to retrieve the output of the 'ps aux' command. So far, this is what I have:
ps aux | sort -r -n -k3 | sed -e '1s/^/this is first\n/' | head -n10
With this I can insert a line at position 1, but I would rather extract the... (3 Replies)
Hi,
I have a file with a header line, followed by some contents. How can I sort the file according to header lines?
eg.
/* abcd_005*/
a
bc
/* abcd_001*/
d
e
/* abcd_002*/
x
y
desired output:
/*abcd_001*/ (0 Replies)
I am having report file with header and footer . The details in between header and footer are separated by a pipe charater. I want to sort the file by considering multiple columns in between header and footer.
pls help (4 Replies)
How to sort a tab delimited file first on col1 and then on col2. Also I need to keep the header intact.
file.txt
val1 val2 val3 val4
a b c d
m n o p
e f g h
i j k l
... (3 Replies)
I have several las files with a header and each file start Version and text and before the data starts end up with ~Ascii, then the numbers starts:
-------------------------------------------------------------------------
Code:
~Version
.....text....
~Ascii
2 abc 230 1 name
1 abc ... (1 Reply)
I have several las files with a header and each file start Version and text and before the data starts end up with ~Ascii, then the numbers starts:
-------------------------------------------------------------------------
~Version
.....text....
~Ascii
2 abc 230 1 name
1 abc 400 1... (17 Replies)
Hi,
I am using SUN SOLARIS (SunOS sun4v sparc SUNW, T5240).
I have a huge data file with header and trailer. This file gets used into an ETL process. ETL skips the header record (which is the first record of the file) and loads the rest of the record. The file can be delimited (comma,... (5 Replies)
Hi ,
My UNIX system is SUN Solaris.
I am trying to do a simple thing as described below.
I have a PIPE delimited file that has header and trailer. So the file is something like below:
Test1.txt looks like something below:
field_data1|field_data2|and some more data --Header
... (5 Replies)
Discussion started by: Saanvi1
5 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)