Hi,
My input file is
$cat samp
1 siva
1 raja
2 siva
1 siva
2 raja
4 venkat
i want sort this name wise...alos need to remove duplicate lines.
i am using
cat samp|awk '{print $2,$1}'|sort -u
it showing
raja 1 (3 Replies)
the rows have to be sorted according to the second column (family name). In addition, the number of family names that start with a particular alphabet
character is put before the beginning of the series. Assume that the file have
4 columns with the following column formatting:
first name... (5 Replies)
Hello,
I've done
ls -ls >fileout1
When I do the sort command for +4 it sorts it bu group. When I do +5 it sorts it by date. But it's skipping the file size column. Example:
rwxr-xr-x 1 Grueben sup 65 16 Sep 13:58 cdee
How can I sort it by file size? It doesn't... (2 Replies)
Hello ,
i have a text file like this
1 a1 ,AB ,AC ;AD ,EE
2 a2 ,WE ;TR ,YT ,WW
3 a3 ;AS ,UY ;RF ,YT
i want to sort this text file based on each row , and excluding 2nd column from the sorting and not taking the comma or ; into consideration in the sorting, so it will become like this... (12 Replies)
Hello everyone!
As the heading reads, I would like to sort the lines of a text file, starting at a specific column (i.e. skip the first X characters of each line).
What I’m actually trying to sort is the md5 sums file of a directory. Every time I copy a new file to that directory, I perform... (3 Replies)
hello, I have a large file (about 1gb) that is in a file similar to the following:
I want to make it so that I can put all the duplicates where column 3 (delimited by the commas) are shown on top. Meaning all people with the same age are listed at the top.
The command I used was ... (3 Replies)
Hello All,
I have a file which have content as below.
03/09/2014 10:35 AM 618 Admin\rick pqr_ klm2_pog12_20140309_c.xlsx
03/10/2014 10:35 AM 618 user\test01 mplz_ fgh2_lal12_20140310_c.xlsx
03/17/2014 10:35 AM 618 Admin\vick abc_ xyz2_bc12_20140317_c.xlsx
03/18/2014 ... (2 Replies)
I have to sort the 4th column of an excel/csv file. I tried the following command
sort -u --field-separator=, --numeric-sort -k 2 -n dinesh.csv > test.csv
But, it's not working. Moreover, I have to do the same for more than 30 excel/csv file. So please help me to do the same. (6 Replies)
I have a csv file as shown below,
xop_thy 80 avr_njk 50 str_nyu 60
avr_irt 70 str_nhj 60 avr_ngt 50
str_tgt 80 xop_nmg 50 xop_nth 40
cyv_gty 40 cop_thl 40 vir_tyk 80
vir_plo 20 vir_thk 40 ijk_yuc 70
cop_thy 70 ijk_yuc 80 irt_hgt 80
I need to align/sort the csv file based... (7 Replies)
Discussion started by: dineshkumarsrk
7 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)