Tweet
samtools merge error underestimating the sequence counts
Counts from pileup from the combined bam of 6 different libraries.
Chr1 5378242 80
Chr1 5378243 112
Chr1 5378244 193
Chr1 5378245 5997 <--- Notice problem from next line
Chr1 5378246 7999
Chr1 5378247 8000
Chr1 5378248 8001
Chr1 5378249 8002
Chr1 5378250 8003
Chr1 5378251 8004
Counts from mpileup with 6 different libraries processed separately
(The third column gives the total counts and the next 6 columns correspond to individual
counts from libraries)
When the total counts are high they are reduced in the combined bam file.
Chr1 5378242 80 43 3 9 3 6 16
Chr1 5378243 112 66 4 10 7 6 19
Chr1 5378244 193 104 6 16 16 22 29
Chr1 5378245 5997 2781 953 563 965 23 712
Chr1 5378246 16714 9388 2914 1268 1854 24 1266 <--- higher counts here
Chr1 5378247 23732 13433 3101 2057 2689 26 2426
Chr1 5378248 32700 18643 3210 3253 3614 26 3954
Chr1 5378249 54741 33457 3581 5158 6788 28 5729
Chr1 5378250 64307 40959 3688 5872 7531 28 6229
Chr1 5378251 70975 45306 3829 6595 8176 29 7040
Chr1 5378242 80
Chr1 5378243 112
Chr1 5378244 193
Chr1 5378245 5997 <--- Notice problem from next line
Chr1 5378246 7999
Chr1 5378247 8000
Chr1 5378248 8001
Chr1 5378249 8002
Chr1 5378250 8003
Chr1 5378251 8004
Counts from mpileup with 6 different libraries processed separately
(The third column gives the total counts and the next 6 columns correspond to individual
counts from libraries)
When the total counts are high they are reduced in the combined bam file.
Chr1 5378242 80 43 3 9 3 6 16
Chr1 5378243 112 66 4 10 7 6 19
Chr1 5378244 193 104 6 16 16 22 29
Chr1 5378245 5997 2781 953 563 965 23 712
Chr1 5378246 16714 9388 2914 1268 1854 24 1266 <--- higher counts here
Chr1 5378247 23732 13433 3101 2057 2689 26 2426
Chr1 5378248 32700 18643 3210 3253 3614 26 3954
Chr1 5378249 54741 33457 3581 5158 6788 28 5729
Chr1 5378250 64307 40959 3688 5872 7531 28 6229
Chr1 5378251 70975 45306 3829 6595 8176 29 7040