set -x showed that, while I am still not sure of the best way to accomplish this, the final vcf.gz that comes from the 001 folder is called variants.vcf.gz. The final vcf.gz that comes from the 002 folder is also called variants.vcf.gz. So unless the files are named differently somehow they are always going to be replaced. Thank you .
Hello cmccabe,
I am sorry, I am confused about your requirement. But by seeing your findcommand I could say you need to copy few files by finding them from one location to another and copy to detination directory, so you could try to change your command with following(not tested though).
It will copy all matched files to destination directory. Please try it and do let us know how it goes then. If your requirement is different then please be more clear and specific in your requirements.
Thanks,
R. Singh
Last edited by RavinderSingh13; 09-20-2016 at 05:38 AM..
Hi,
I am newbie in UNIX so please excuse for my questions.
Is there a a way to search for string in files within folder and sub folder in particluar file extensions.
Ex. search for ABC in folder 'A'(including it's sub folders) in html, xml files.
Thanks,
Ani (2 Replies)
Hi,
I need to search for some strings in specific positions in a file.
If the strings: "foo1", "foo2" or "foo3" is on position 266 or position 288 in a file i want the whole line printed.
Any idea how to do it? (5 Replies)
Hi All,
I was exploring find command and came across -prune option which would exclude search in a mention subdirectory.
My quesry is to search all files more that 100 MB size but exclude search in a subdirectory.
I am using below command,but somehow it is not working.
Can anybody help me... (6 Replies)
Ok question number two: I'd like to search a directory for multiple file types (rar, txt, deb) and depending on what's found, copy those files to folders named Rar, TextFiles, and Debs. I'm looking for speed here so the faster the script the better. I want it to be a function that I pass 1 argument... (4 Replies)
Hi I made this code to search in directory for file and size
How can I remodel it to seach in the sub direcotry as well
Thanks
#!/bin/bash
echo -n "Enter: "
read var
if
then
echo "Directory exists: ${var}"
size=`du -hs "${var}"`
echo The size of the current folder is... (4 Replies)
Hi,
I have a script that handles a huge amount of log files from many machines and copies it into a SAN location with the following directory structure:
/SAN/machinenames/yyyy/m/d
so for example
/SAN/hosta/2011/3/12/files*
Now I am writing a bash script to search for files between to date... (4 Replies)
hi I want to write a script which count the number of subdirectories in the current root directory that contain more than a specified number of files of a specific type. Is there an easy way to do this?
Thanks
Robert (2 Replies)
I have a simple function that greps within a folder into files that are already gunzipped. This was already written for me so from my understanding fn=$1 specifies that it will look into any file in that folder that is gunzipped and the rest of the script greps the data its looking for and puts it... (3 Replies)
I am trying to write a script that cycles through a folder containing many folders and when inside each one it's supposed to copy all the .fna.gz files to a folder elsewhere if the file and the respective folder have the same name.
for fldr in /home/playground/genomes/* ; do
find .... (8 Replies)
Lets say I have a massive directory which is filled with other directories all filled with different c++ scripts and I want a listing of all the scripts that contain the string: "this string". Is there a way to use a grep search for that? I tried:
grep -lr "this string" *
but I do not... (3 Replies)
Discussion started by: Circuits
3 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)