How to prepare a FASTA file for calling SNP by GATK

[1] bedtools (https://github.com/arq5x/bedtools2) here is also bedtools (https://github.com/arq5x/bedtools2) getfasta. It uses Erik's code under the hood. $ cat test.fa >chr1 AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG $ cat test.bed chr1 5 10 $ be

今天运行tophat2的时候看到下面这条记录: [2016-02-27 11:40:03] Checking for reference FASTA file Warning: Could not find FASTA file /home/pub/database/Human/hg19/bowtie2_db/hg19.fa.fa [2016-02-27 11:40:03] Reconstituting reference FASTA file from Bowtie index Executi

from gff3 get gene fasta sequence ,or promoter sequence #taken from https://www.biostars.org/p/46281/ and modified as needed 10/15/15 use strict; use warnings; use Bio::Seq; use Bio::SeqIO; use Bio::DB::Fasta; #add a help message here #my $num_args=$

Use a regular expression for filtering sequences by id from a FASTA file, e.g. just certain chromosomes from a genome. There are other tools as part of bigger packages to install (and no regex support), mostly awk-based awkward (sorry for the pun) ba

原文:http://wiki.wxpython.org/Getting%20Started 1. 第一个应用程序:Hello World 按照“国际惯例”,我们先写一个“Hello World”的应用程序,下面是代码: 1 #!/usr/bin/env python 2 import wx 3 4 app = wx.App(False) # Create a new app, don't redirect stdout/stderr to a window. 5 frame = wx.Frame

海宝建议用这个拼接软件 http://www.broadinstitute.org/software/discovar/blog/?page_id=98 DISCOVAR – variant caller 适合于call variant 和拼接小基因组 DISCOVAR de novo 适合拼接大基因组 下载: ftp://ftp.broadinstitute.org/pub/crd/DiscovarDeNovo/latest_source_code/LATEST_VERSION.tar.gz

一.ActivityManagerService提供的主要功能: (1)统一调度各应用程序的Activity (2)内存管理 (3)进程管理 二.启动一个Activity的方式有以下几种: (1)在应用程序中调用startActivity启动指定的Activity (2)在Home程序中单击一个应用图标,启动新的Activity (3)按"Back"键,结束当前Activity,返回到上一个Activity (4)长按"Home"键,显示出当前正在运行的程序列表,从

http://blog.sciencenet.cn/blog-1469385-819498.html 文章目录 一.准备工作 二.流程概览 三.流程 首先说说GATK可以做什么.它主要用于从sequencing 数据中进行variant calling,包括SNP.INDEL.比如现在风行的exome sequencing找variant,一般通过BWA+GATK的pipeline进行数据分析. 要run GATK,首先得了解它的网站(http://www.broadinstitute.org/

Index NAME SYNOPSIS EXAMPLE PROGRAM ABOUT THIS DOCUMENT WHAT TO READ WHEN IN A HURRY ABOUT LIBEV FEATURES CONVENTIONS TIME REPRESENTATION ERROR HANDLING GLOBAL FUNCTIONS FUNCTIONS CONTROLLING EVENT LOOPS ANATOMY OF A WATCHER GENERIC WATCHER FUNCTIONS