Chris Fields cjfields

## 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

## rt-to-github.pl
#!/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;

## entrenzgeneid
#!/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 => 'mymail@foo.bar',
	*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
	#!/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;
	#!/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 => 'mymail@foo.bar',