cjfields

*bcftools filter
*Filter variants per region (in this example, print out only variants mapped to chr1 and chr2)
qbcftools filter -r1,2 ALL.chip.omni_broad_sanger_combined.20140818.snps.genotypes.hg38.vcf.gz

*printing out info for only 2 samples:
bcftools view -s NA20818,NA20819 filename.vcf.gz

*printing stats only for variants passing the filter:
bcftools view -f PASS filename.vcf.gz

cjfields

### Keybase proof

I hereby claim:

  * I am cjfields on github.
  * I am cjfields1 (https://keybase.io/cjfields1) on keybase.
  * I have a public key ASDPcg3zKQhuM4zlwlgr_WT51Zx3af3gDmZiDfaAP6wCTQo

To claim this, I am signing this object:

cjfields

#!/usr/bin/env perl
use v5.10;
use strict;
use warnings;
use Carp;
use IO::Prompt::Tiny 'prompt';
use Net::GitHub;
use Path::Tiny;
use RT::Client::REST::Ticket;
use RT::Client::REST;

cjfields

<Data><Node><name>localhost</name><state>down</state><power_state>Running</power_state><np>1</np><ntype>cluster</ntype><mom_service_port>15002</mom_service_port><mom_manager_port>15003</mom_manager_port></Node><Node><name>compute-0-0</name><state>free</state><power_state>Running</power_state><np>24</np><properties>default</properties><ntype>cluster</ntype><status>rectime=1490961583,macaddr=c8:1f:66:e7:ed:a7,cpuclock=Fixed,varattr=,jobs=,state=free,netload=1027239438175,gres=,loadave=0.03,ncpus=24,physmem=198441684kb,availmem=197699068kb,totmem=199465676kb,idletime=1444659,nusers=0,nsessions=0,uname=Linux compute-0-0.local 2.6.32-431.11.2.el6.x86_64 #1 SMP Tue Mar 25 19:59:55 UTC 2014 x86_64,opsys=linux</status><mom_service_port>15002</mom_service_port><mom_manager_port>15003</mom_manager_port></Node><Node><name>compute-1-0</name><state>free</state><power_state>Running</power_state><np>24</np><properties>cuda</properties><ntype>cluster</ntype><status>rectime=1490961584,macaddr=b8:2a:72:d6:7b:58,cpuclock=Fixed,

cjfields

[cjfields@cjfields-imac zef (master)]$ zef install Inline::Perl5
===> Searching for: Inline::Perl5
===> Building: Inline::Perl5:ver('0.22'):auth('github:niner')
In file included from p5helper.c:2:
In file included from /Users/cjfields/perl5/perlbrew/perls/perl-5.20.1t/lib/5.20.1/darwin-thread-multi-2level/CORE/perl.h:5188:
/Users/cjfields/perl5/perlbrew/perls/perl-5.20.1t/lib/5.20.1/darwin-thread-multi-2level/CORE/inline.h:311:9: warning: nonnull parameter 'pv' will evaluate to 'true' on first encounter [-Wpointer-bool-conversion]
    if (pv && len > 1) {
        ^~ ~~
1 warning generated.
===> Building [OK] for Inline::Perl5:ver('0.22'):auth('github:niner')

cjfields

[cjfields@cjfields-imac zef (master)]$ zef install Inline::Perl5
===> Searching for: Inline::Perl5
===> Searching for missing dependencies: File::Temp
===> Searching for missing dependencies: File::Directory::Tree
===> Building: Inline::Perl5:ver('0.15'):auth('github:niner')
===> Building [OK] for Inline::Perl5:ver('0.15'):auth('github:niner')
===> Testing: File::Directory::Tree:auth('labster')
t/basic.t .. ok
All tests successful.
Files=1, Tests=7,  0 wallclock secs

cjfields

[cjfields@cjfields-imac ~]$ perl6
You may want to `panda install Readline` or `panda install Linenoise` or use rlwrap for a line editor

To exit type 'exit' or '^D'
> try '2**10000000000'.EVAL; say $!.^name
X::Numeric::Overflow

cjfields

[cjfields@Chriss-MacBook-Air bioperl6]$ time perl fasta.pl sequence.fasta
Count: 12097

real   	0m0.434s
user   	0m0.416s
sys    	0m0.014s
[cjfields@Chriss-MacBook-Air bioperl6]$ time perl6 fasta.pl6 sequence.fasta
Count: 12097

real   	0m4.406s

cjfields

[cjfields@Chriss-MacBook-Air bioperl-live (master)]$ ./Build test
t/Align/AlignStats.t ................... ok
t/Align/AlignUtil.t .................... ok
t/Align/Graphics.t ..................... skipped: The optional module GD (or dependencies thereof) was not installed
t/Align/SimpleAlign.t .................. ok
t/Align/TreeBuild.t .................... ok
t/Align/Utilities.t .................... ok
t/AlignIO/AlignIO.t .................... ok
t/AlignIO/arp.t ........................ ok
t/AlignIO/bl2seq.t ..................... ok

cjfields

(Python3)[cjfields@cjfields-imac bioperl6 (master)]$ prove6 -lrv t/SeqIO.t
t/SeqIO.t ..
ok 1 -
===SORRY!===
No such method 'update' for invocant of type 'Signature'
ok 2 - format
ok 3 - readonly
ok 4 - version
ok 5 - variant
ok 6 - format