Hello
Regarding the number of reads covering a position in a .bam alignment file, my understanding is that 'samtools depth' and 'samtools mpileup' output should represent the same thing. From what I've read up their respective explanations are :
depth: " compute the per-base depth"
mpileup: "the number of reads covering the site"
However, I am getting different numbers when these options are run on the same .bam file (which is a paired end alignment file).
For example looking at the last 5 lines of each:
Depth:
samtools depth aln.bam | tail -n 5
samp2 5819 46
samp2 5820 46
samp2 5821 45
samp2 5822 43
samp2 5823 43
mpileup (omitting the last fields):
$ samtools mpileup -f ../samp2.fa aln.bam | tail -n 5
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
samp2 5819 C 24
samp2 5820 A 24
samp2 5821 T 24
samp2 5822 G 23
samp2 5823 A 23
Probably a simple reason I am missing. Would someone be able to clarify?
Thanks
Regarding the number of reads covering a position in a .bam alignment file, my understanding is that 'samtools depth' and 'samtools mpileup' output should represent the same thing. From what I've read up their respective explanations are :
depth: " compute the per-base depth"
mpileup: "the number of reads covering the site"
However, I am getting different numbers when these options are run on the same .bam file (which is a paired end alignment file).
For example looking at the last 5 lines of each:
Depth:
samtools depth aln.bam | tail -n 5
samp2 5819 46
samp2 5820 46
samp2 5821 45
samp2 5822 43
samp2 5823 43
mpileup (omitting the last fields):
$ samtools mpileup -f ../samp2.fa aln.bam | tail -n 5
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
samp2 5819 C 24
samp2 5820 A 24
samp2 5821 T 24
samp2 5822 G 23
samp2 5823 A 23
Probably a simple reason I am missing. Would someone be able to clarify?
Thanks
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