0 depth in pileup files from BAM files ?

[jjlaisnoopy]

Hi, guys:

After I pileup my BAM file to get depth and coverage from the alignment data, I found some wired things came out. There are about 10% base positions with 0 depth. What is this? Could someone give me hand to get the real depth of coverage? Thanks in advance.

[swbarnes2]

Hi, guys:

After I pileup my BAM file to get depth and coverage from the alignment data, I found some wired things came out. There are about 10% base positions with 0 depth. What is this? Could someone give me hand to get the real depth of coverage? Thanks in advance.

Why don't you believe your own data?

[jjlaisnoopy]

Hi, guys:

After I pileup my BAM file to get depth and coverage from the alignment data, I found some wired things came out. There are about 10% base positions with 0 depth. What is this? Could someone give me hand to get the real depth of coverage? Thanks in advance.

Sorry, maybe I should clarify this part. I mean , in coverage regions, there are about 10% bases positions with 0 depth , not in bases of whole reference genome.

[Heisman]

If you look at those regions in IGV, do the bases that are said to have 0x coverage appear to have 0x coverage? Are you 100% convinced they do not have 0x coverage? If so, maybe post the commands you used.