My input:
File_1:
2000_t
g1110.b1
abb.1
2001_t
g1111.b1
abb.2
abb.2
g1112.b1
abb.3
2002_t
.
.
File_2:
2000_t Ali england 135
abb.1 Zoe british 150
2001_t Ali england 305
g1111.b1 Lucy russia 126 (6 Replies)
Hi all,
This is actually more for my lazyness then anything else, but I think others might find it useful to use as well. Basically this is what I am trying to achieve...
In my ubuntu home dir under Downloads is where firefox saves everything by default, now I know that you can manually... (3 Replies)
Move all files starting with a specific name to different directory.
This shell script program should have three parameters
File Name
Source Directory
Destination Directory
User should be able to enter ‘AB_CD*' in file name parameter. In this case all the files starting with AB_CD will... (1 Reply)
Hi Folks,
I have different type of file in my current directory. From my current directory i need to move the file which is start with csp_rules and if the file is having the string payg , then I need to move all this files to another directory /output/record. Please help me how to do this?
... (3 Replies)
Hi All,
Really stuck up with a requirement where I need to move a file (Lets say date_Employee.txt--the date will have different date values like 20120612/20120613 etc) from one directory to another based on creation/modification dates.
While visiting couple of posts, i could see we can... (3 Replies)
Hi all,
I'm new to this forum and bash scripting. I have the following problem, I need to copy some files (from one dir. to another) whose first 5 numbers (subjects' ID) match the directory names. Here a shortened version of what I'm trying to do:
names=(32983_f 35416_f 43579_f) # these are... (6 Replies)
I am using bash to prompt a user for a choice using: where a "y" response opens a menu with available panels that can be used.
while true; do
read -p "Do you want to get coverage of a specific panel?" yn
case $yn in
* ) menu; break;;
* ) exit;;
* ) echo... (6 Replies)
I have a specific set (all ending with .bam) of downloaded files in a directory /home/cmccabe/Desktop/NGS/API/2-15-2016. What I am trying to do is use a match to $2 in name to rename the downloaded files. To make things a more involved the date of the folder is unique and in the header of name... (1 Reply)
I have a directory /home/cmccabe/nfs/exportedReports that contains multiple folders in it. The find writes the name of each folder to out.txt. A new directory is then created in a new location /home/cmccabe/Desktop/NGS/API, named with the date. What I am trying to do, unsuccessfully at the moment,... (7 Replies)
In the below bash I am trying to rename eachof the 3 text files in /home/cmccabe/Desktop/percent by matching the numerical portion of each file to lines 3,4, or 5 in /home/cmccabe/Desktop/analysis.txt. There will always be a match between the files. When a match is found each text file in... (2 Replies)
Discussion started by: cmccabe
2 Replies
LEARN ABOUT DEBIAN
vcf-compare
VCF-COMPARE(1) User Commands VCF-COMPARE(1)NAME
vcf-compare - compare bgzipped and tabix indexed VCF files
SYNOPSIS
compare-vcf [OPTIONS] file1.vcf file2.vcf ...
DESCRIPTION
About: Compare bgzipped and tabix indexed VCF files. (E.g. bgzip file.vcf; tabix -p vcf file.vcf.gz)
OPTIONS -c, --chromosomes <list|file>
Same as -r, left for backward compatibility. Please do not use as it will be dropped in the future.
-d, --debug
Debugging information. Giving the option multiple times increases verbosity
-H, --cmp-haplotypes
Compare haplotypes, not only positions
-m, --name-mapping <list|file>
Use with -H when comparing files with differing column names. The argument to this options is a comma-separated list or one mapping
per line in a file. The names are colon separated and must appear in the same order as the files on the command line.
-R, --refseq <file>
Compare the actual sequence, not just positions. Use with -w to compare indels.
-r, --regions <list|file>
Process the given regions (comma-separated list or one region per line in a file).
-s, --samples <list>
Process only the listed samples. Excluding unwanted samples may increase performance considerably.
-w, --win <int>
In repetitive sequences, the same indel can be called at different positions. Consider records this far apart as matching (be it a
SNP or an indel).
-h, -?, --help
This help message.
vcf-compare 0.1.5 July 2011 VCF-COMPARE(1)