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Old 07-19-2011, 02:22 PM   #1
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Location: San Francisco

Join Date: Jun 2011
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Question *** Per base coverage ***

This seems like a silly question, but I can't quite find the answer for it anywhere. I have a list of single nucleotide position, ie,
chr 1 72342
chr 2 32912
chr X 184343
to which I would like to find their coverage, ie, how many reads cover that position and what are those bases.
This is almost like calling SNP, but not quite because I just like to know the coverage even if no SNP is present. For this reason, I can't just use a SNP caller. Does anyone have a solution for this?
Thanks so much.
cristae8 is offline   Reply With Quote
Old 07-19-2011, 05:20 PM   #2
Location: nevada

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I loaded all my short read data into an SQL database so that this information can be pulled out with a quick query.

For example, to find how many reads cover position 72342 of chr 1, just type in the following query. This assumes 50bp reads.

select count(*) from short_reads
where (chromosome = 'chr1')
and (start_position >= 72293)
and (start_position <= 72342)

To perform this query for many SNPs, a PERL script can be written.
kwatts59 is offline   Reply With Quote
Old 07-19-2011, 08:26 PM   #3
Location: Melbourne

Join Date: Jun 2010
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The coverageBed function in bedtools ( should be able to do what you want.
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Old 07-19-2011, 09:55 PM   #4
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you can use samtools pileup -c from on sorted indexed bam file of your alignment..this pileup consensus will give you read depth in each position and base composition in each also
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Old 07-21-2011, 02:50 PM   #5
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Thanks, everyone. bedTools seems to work the best and it's fully documented so very easy to use! Much thanks to Aaron (the author) & Pete.
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Old 07-21-2011, 04:11 PM   #6
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samtools view -b <in.bam> <chr>:<pos>-<pos> | samtools pileup - | grep <pos> | awk '{print $4}'
Mendelian Disorder: A blogshare of random useful information for general public consumption. [Blog]
Breakway: A Program to Identify Structural Variations in Genomic Data [Website] [Forum Post]
Projects: U87MG whole genome sequence [Website] [Paper]
Michael.James.Clark is offline   Reply With Quote

per base coverage

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