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Old 04-21-2012, 01:48 AM   #1
jjlaisnoopy
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Default 0 depth in pileup files from BAM files ?

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.
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Old 04-21-2012, 10:20 PM   #2
swbarnes2
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Quote:
Originally Posted by jjlaisnoopy View Post
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?
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Old 04-22-2012, 12:18 AM   #3
jjlaisnoopy
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Quote:
Originally Posted by jjlaisnoopy View Post
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.
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Old 04-22-2012, 08:38 AM   #4
Heisman
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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.
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