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Samtools for SNPs and InDels  

2011-03-22 21:57:42|  分类: 生物信息分析 |  标签: |举报 |字号 订阅

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          一下是台湾黄耀庭教师实验室有关SAMtools的简介,引在这里和大家学习。
       Samtools homepage recommends snp calling with the following command:

1. samtools mpileup -uf ref.fa aln1.bam aln2.bam | bcftools view -bvcg - > var.raw.bcf
2. bcftools view var.raw.bcf | vcfutils.pl varFilter -D100 > var.flt.vcf

   Samtools 簡介

軟體簡介 Samtools is an application for detecting SNP and small indels
突變偵測 SNP / indel
核心技術 [Bayes' theorem]
原創作者 Li H, et al
維護狀況 0.1.8 - 2010/07/12
輸入格式 BAM / SAM
輸出格式 Samtools default format / MAQ format
適用機器架構 i386 / x86_64
作業平台 Linux / Windows

Another information

http://samtools.sourceforge.net/samtools.shtml
http://samtools.sourceforge.net/cns0.shtml

The problem of huge amount of false-positive SNPs/indels has been reported. When indels occur towards the ends of reads, the alignment can lead to false SNPs as well as improperly placed indels. Local re-alignment is suggested.
http://seqanswers.com/forums/showthread.php?t=4234
Indels are hard to align so all reads agree, since each read is aligned independently. Efforts have been made in GATK to create an local re-aligner; I have my own (now not so stealth) effort. These both help SNP calling, as mis-aligned reads with indels leads to false SNPs, as well as to form a better consensus around indels. Regarding the SNP quality, I usually see upwards of 255 for some SNPs, but indels are off the chart and can reach >2000.
http://www.broadinstitute.org/gsa/wiki/index.php/Local_realignment_around_indels
http://sourceforge.net/apps/mediawiki/srma/index.php?title=Main_Page
SNPs should be mostly correct in SOLid because of SOLid's dibase sequencing. But indels are not benefited from dibase sequencing.

相關連結

more information pls link to:http://bioinfo.cs.ccu.edu.tw/wiki/doku.php?id=samtool_for_indels
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