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htslib和Samtool安装步骤（一）htslib安装：参考【1】1.下载：git clone https://github.com/samtools/htslib.git2.安装指令：autoconf # Generate the configure script, if needed./configure # Optional,

很多地方都有这个连接：samtools的说明文档：http://samtools.sourceforge.net/samtools.shtml但是连不上了，所以现在的地址为：http://www.htslib.org/doc/samtools.html分析原因：连接超时samtools.sourceforge.net 的服务器响应时间过长。 此站点暂时不可用或者太

问题之htslib安装时没有zlib问题：HTSlib uses compression routines from the zlib library .Building HTSlib requires zlib development files to be installed on the buildmachine; you may need to ensure a package

使用samtools来对sam/bam/cram相互转换sam bamsamtools view -h NA12878.bam >NA12878_2.sam samtools view -b -S NA12878.sam > NA12878_2.bam samtools view -C -T ref.fa aln.bam > aln.cramsamtoo

1.Samtools的help：hadoop@Mcnode1:~/cloud/adam/xubo/data/data_HDFS/adam$ samtools --helpProgram: samtools (Tools for alignments in the SAM format)Version: 1.3-20-gd49c73b (using htslib 1.3-35-g26b30

SAM格式：1.FLAG说明： Each bit in the FLAG field is defined as:0x0001 p the read is paired in sequencing0x0002 P the read is mapped in a proper pair0x0004 u the query sequence itself is unmap

SAM数据格式学习3之官方文档http://samtools.github.io/hts-specs/SAMv1.pdf其他详细格式：https://github.com/samtools/hts-specs里面很详细

SAM信息中的一条：SRR003161.2 0 chr7 41381016 60 4S153M1D132M1D5M1D28M1D73M3I12M1I40M54S * 0 0 TCAGTTTGAGATGGAGTTTCATTCTTGTTGCCCAGGCTGGAGTGCAATGGCGCAATCTCAGCTCACAGCAACCTCCGCCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCC