sequenza细胞纯度计算

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

··········································································································

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

··························································································