Extract base information from aligned reads in a sam file

Question

[yliueagle]

I generated a sam (bam) file by aligning fastq to reference using BWA. Now I would like to retrieve the the basepair at a given chromosome position, for example, chr12:11010100:11010100, for all reads aligned to this region, how can I do that? Thanks! (My expected workflow would be: (1) extract reads from sam that cover the querying position; (2) get the basepair from these reads at this position)

[GenoMax]

Look into using igvtools which is part of IGV. I assume you are looking to get counts of basepairs (alleles) at a particular location.

[yliueagle]

Not only counts, but the basepair at that position for each read, with read name included in the output. (Of course the counts can be generated from this table as a downstream step)

[Kevin Blighe]

Due to the fact that NGS data is very 'messy' (désordonnée), every base position will have multiple bases. You may want to output the frequencies of these via: A: Calculate The Frequency Of Nucleotides At Each Position In An Mpileup File

[JC]

Is this good enough? samtools view <your bam> chr:start-end > reads.sam

[GenoMax]

That will get the reads but not specific base at that position. Not sure what is the best way to do that.

[yliueagle]

Thank you. This do obtain the reads but I also need to retrieve the basepair information from reads.sam at chr:start-end

Answer 1

[yliueagle]

I found http://lindenb.github.io/jvarkit/Sam2Tsv.html can do the job. Thanks all!