Get Phred Score/Base Quality for BAM File Per base
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Entering edit mode
17 months ago
gtasource ▴ 60

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

phred score • 810 views
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Entering edit mode
17 months ago

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

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