samtools mpileup -uf ref.fa aln.bam | bcftools view -cg – | vcfutils.pl vcf2fq > cns.fq
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#!/usr/bin/perl -w use strict; use Bio::SeqIO; use Bio::Seq::Quality; use Getopt::Long; die “pass a fasta and a fasta-quality file\n” unless @ARGV; my ($seq_infile,$qual_infile) = (scalar @ARGV == 1) ?($ARGV[0], “$ARGV[0].qual”) : @ARGV; ## Create input objects for both a seq (fasta) and qual file my $in_seq_obj = Bio::SeqIO->new( -file => $seq_infile, -format => ‘fasta’, ); my […] #!/usr/bin/env perl # Convert a fastq to a fasta/qual combo using BioPerl, with some Linux commands use Bio::Perl; use Data::Dumper; use strict; use warnings; use threads; use Thread::Queue; use Getopt::Long; my $settings={}; $|=1; my %numSequences; # static for a subroutine exit(main()); sub main{ die(“Usage: $0 -i inputFastqFile [-n numCpus -q outputQualfile -f outputFastaFile]”) if(@ARGV<1); GetOptions($settings,(‘numCpus=s’,’input=s’,’qualOut=s’,’fastaOut=s’)); […] |
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