Get Phred Score/Base Quality for BAM File Per base

Question

[gtasource]

Hi all,

I have a BAM file I'm try to get some base quality scores from in the form of a bed file. I have used QualityScoreDistribution from GATK, and that works at giving overall scores, but not per base metric. To explain this a little better:

I have a BAM file and an associated BED file for the sequences I want to get phred scores from. If I could somehow use these two files, and then generate a file that has Chromosome Pos and Phred Score.

If anybody could point me in the right direction? Thanks

Answer 1

[Pierre Lindenbaum]

Use samtools mpileup to get all the qualities at a given position.