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Old 02-02-2015, 03:50 PM   #1
M4TTN
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Default Frequency of A, C, T, or G at every position in SAM file

Dear all,

We would like to extract the read depth of each base type (A, C, T or G) for every position of our aligned reads (a SAM file created using Bowtie2).

Does anyone know of a tool that does this?

The closest link I found here was:
http://seqanswers.com/forums/showthread.php?t=38630

But I'm not sure that would be appropriate for use with aligned genome data.

Many thanks
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Old 02-02-2015, 11:49 PM   #2
dariober
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Hi- I think pysamstats can do what you need.
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Old 02-03-2015, 02:19 AM   #3
M4TTN
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Dear dariober,

We've got pysamstats up and running and it seems to be generating exactly the kind of output we require!

Many thanks for your help, Matt
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