samtools 实现对bam文件统计测序深度 和 比对率
001、利用samtools计算每一个位点的测序深度
[b20223040323@admin1 test]$ ls ## 测试bam文件 SRR21814498.sorted.markdup.bam SRR21814498.sorted.markdup.bam.bai [b20223040323@admin1 test]$ samtools depth -aa SRR21814498.sorted.markdup.bam > all_depth.txt ## 利用samtools统计参考基因组所有位点的测序深度 [b20223040323@admin1 test]$ ls ## 结果文件 all_depth.txt SRR21814498.sorted.markdup.bam SRR21814498.sorted.markdup.bam.bai [b20223040323@admin1 test]$ head all_depth.txt ## 查看前10行 NC_003070.9 1 0 NC_003070.9 2 0 NC_003070.9 3 0 NC_003070.9 4 0 NC_003070.9 5 0 NC_003070.9 6 0 NC_003070.9 7 0 NC_003070.9 8 0 NC_003070.9 9 0 NC_003070.9 10 0
002、统计比对到参考基因组的位点的平均测序深度
[b20223040323@admin1 test]$ ls all_depth.txt SRR21814498.sorted.markdup.bam SRR21814498.sorted.markdup.bam.bai [b20223040323@admin1 test]$ head all_depth.txt ## 所有位点的测序深度信息 NC_003070.9 1 0 NC_003070.9 2 0 NC_003070.9 3 0 NC_003070.9 4 0 NC_003070.9 5 0 NC_003070.9 6 0 NC_003070.9 7 0 NC_003070.9 8 0 NC_003070.9 9 0 NC_003070.9 10 0 [b20223040323@admin1 test]$ awk -F "\t" 'BEGIN{a = 0; b = 0} {if($3 > 0) {a++; b += $3}} END {print b/a}' all_depth.txt ## 统计测到的位点的平均的测序深度 9.88724
003、统计基因组所有位点,包括未测到的位点的平均测序深度
[b20223040323@admin1 test]$ ls all_depth.txt SRR21814498.sorted.markdup.bam SRR21814498.sorted.markdup.bam.bai [b20223040323@admin1 test]$ head all_depth.txt NC_003070.9 1 0 NC_003070.9 2 0 NC_003070.9 3 0 NC_003070.9 4 0 NC_003070.9 5 0 NC_003070.9 6 0 NC_003070.9 7 0 NC_003070.9 8 0 NC_003070.9 9 0 NC_003070.9 10 0 [b20223040323@admin1 test]$ awk -F "\t" 'BEGIN{a = 0} {if($3 > 0) {a += $3}} END {print a/NR}' all_depth.txt ## 统计参考基因组所有位点平均测序深度 8.84949
004、统计覆盖度
[b20223040323@admin1 test]$ ls all_depth.txt SRR21814498.sorted.markdup.bam SRR21814498.sorted.markdup.bam.bai [b20223040323@admin1 test]$ head all_depth.txt NC_003070.9 1 0 NC_003070.9 2 0 NC_003070.9 3 0 NC_003070.9 4 0 NC_003070.9 5 0 NC_003070.9 6 0 NC_003070.9 7 0 NC_003070.9 8 0 NC_003070.9 9 0 NC_003070.9 10 0 [b20223040323@admin1 test]$ awk -F "\t" 'BEGIN{a = 0} {if($3 > 0) {a++}} END {print a/NR}' all_depth.txt ## 统计测序覆盖度 0.895042
参考:https://www.jianshu.com/p/60b0fda0a591