Extracting base coverage and quality values from BAM files

[unagaswamy]

Experts,
I am interested in extracting base coverage and quality values for non SNP reads from a BAM file?
Thanks,
-Uma

[wenhuang]

pileup in samtools may be what you need.

[bioinfosm]

Yes, pileup is the tool from samtools to display coverage / quality information

[unagaswamy]

Thanks for the info.
Here is what I have tried so far to view the file for a given sample:
samtools view filename.bam chr:start-end

For non SNP positions, I am getting the base coverage using the following command:
samtools view filename.bam chr:start-end |wc -l

Sometimes the actual position is missing when I grep it and ~50 bases around it are printed. My question is how can I trust the wc -l value for a position if that position itself is missing in the BAM file?

[unagaswamy]

Hi Experts,
Can anyone tell me how to extract the base quality from the CQ field of the BAM file? I colleague of mine mentioned that every two ASCII character corresponds to the SOLiD color space. Do I take the average of every overlapping 2 or the max? Any input in this regard is gretaly appreciated!

[nilshomer]

Hi Experts,
Can anyone tell me how to extract the base quality from the CQ field of the BAM file? I colleague of mine mentioned that every two ASCII character corresponds to the SOLiD color space. Do I take the average of every overlapping 2 or the max? Any input in this regard is gretaly appreciated!

Is the base quality not already reported in the SAM record (it should be)? As to how to calculate the base qualities during alignment from color qualities, here is the formula MAQ/BWA/BFAST uses: https://sourceforge.net/apps/mediawi...apping_Quality.

[unagaswamy]

Hi nilshomer,
Thanks for the reply. We are generating SAM record only for the SNP positions which does have the base quality. I am interested in the Non-SNP positions as well and hence I'm trying to calcuate the base quality for these positions from the BAM file.
-Uma

[unagaswamy]

Hi All,
I generated a raw pileup for all reference positions using the samtools. An exmaple record for a non-SNP position is below:
chrY 11936864 G G 51 0 60 8 ,,.,,,.. "%`".B"`

This base has a coverage of 8. Which one of these fields (51,0,60) represent the base quality in this case? I am still confused about the ABI's SOLiD base quality!

Any input is greatly appreciated!

[Bruins]

Did you see the SAM FAQ?

http://sourceforge.net/apps/mediawiki/samtools/index.php?title=SAM_FAQ#I_do_not_understand_the_columns_in_the_pileup_output.

Hope this helps.

[unagaswamy]

Hi Bruins,
Thanks for this very useful link. It definitely answers some of my questions.
-Uma