本文介绍了如何使用Python和R语言的sequenza工具计算细胞纯度。首先，通过samtools生成pileup文件，然后使用sequenza-utils.py进行预处理，包括生成GC内容文件和seqz文件。接着在R环境中加载sequenza库，读取seqz文件并进行GC校正深度比的绘图和直方图分析。最后，通过sequenza.extract和sequenza.fit进行分析并导出结果。
安装sequenza
bam文件要放在前面，否侧会-f命令可能识别错误
samtools mpileup a.bam -f hg19.fasta -Q 20 |gzip > normal.pileup.gz
samtools mpileup b.sorted.bam -f hg19.fasta -Q 20 |gzip > tumor.pileup.gz
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将R语言里sequenza里的sequenza-utils.py复制到/usr/local/bin/下
运行：
#Generating a genome-wide GC content file
python sequenza-utils.py GC-windows -w 50 hg19.fasta |gzip > hg19.gc50Base.txt.gz
#Generate a seqz file
python sequenza-utils.py pileup2seqz -gc hg19.gc50Base.txt.gz -n normal.pileup.gz -t tumor.pileup.gz |gzip > out.seqz.gz
#Trim the seqz file
python sequenza-utils.py seqz-binning -w 50 -s out.seqz.gz | gzip > out_small.seqz.gz
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