Hey,
While doing mpileup, I could see that lot of reads are not counted in mpileup output although I could see them in tview,
I am using following command:
(BTW: I have this problem in all coverage, so its not because of -d flag)
I understood from this link that in samtools tview underlined reads are orphan therefore not counted in mpileup. Is there any way NOT to consider any parameter but to get the complete count at each site
Thank you very much
While doing mpileup, I could see that lot of reads are not counted in mpileup output although I could see them in tview,
I am using following command:
Code:
samtools mpileup -d 10000 -f Ref.fasta accepted_hits.bam > mpileup
I understood from this link that in samtools tview underlined reads are orphan therefore not counted in mpileup. Is there any way NOT to consider any parameter but to get the complete count at each site
Thank you very much
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