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Chris Fields cjfields

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cjfields / BCFtools cheat sheet
Created September 9, 2022 04:10 — forked from elowy01/BCFtools cheat sheet
BCFtools cheat sheet
*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
cjfields / rt-to-github.pl
Created September 16, 2017 17:30 — forked from markstos/rt-to-github.pl
Based on [this copy of rt-to-github.pl](http://www.dagolden.com/index.php/1938/how-to-move-cpan-rt-tickets-to-github/) with the following updates: - The beginnings of a "dry run" mode. Currently just some "say" lines that you have manually uncomment, and comment out the related active lines - Support for importing comments (needs tested) - Bette…
#!/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
cjfields / entrenzgeneid
Created March 8, 2012 18:06 — forked from anonymous/entrenzgeneid
EntrezGeneID get sequence
#!/usr/bin/perl
use strict;
use warnings;
use Bio::DB::EUtilities;
# this needs to be a list of EntrezGene unique IDs
my @ids = @ARGV;
my $eutil = Bio::DB::EUtilities->new(-eutil => 'esearch',
-email => '[email protected]',