Qual Versus Bq Tag In Sam/Bam

Question

[Fixee]

I've noticed in many of the 1000genome BAMs there are qual strings (Phred), one per base, giving base quality; then there is a BQ tag at the end of the read giving base alignment quality.

What's the difference here? Is the first from the sequencing machine giving confidence on the base call and the second from the assembler saying how good the alignment is?

If true, it seems silly to try and give an alignment quality score for each base.

[Jeremy Leipzig]

please paste in a sample line of this BAM/SAM so people can see what you're talking about

Answer 1

[Istvan Albert]

I have not needed to make use of this measure in my work but it intrigued me so I researched it a bit:

From the SAM format specification:

BQ = offset to base alignment quality (BAQ), of the same length as the read sequence. At the i-th read base, BAQi = Qi - (BQi - 64) where Qi is the i-th base quality.

The samtools manual states that:

Base Alignment Quality (BAQ) is a new concept deployed in samtools-0.1.9+. It aims to provide an efficient and effective way to rule out false SNPs caused by nearby INDELs.The BAQ is the Phred-scaled probability of a read base being misaligned.

Answer 2

[lh3]

• Google base alignment quality.

• In the middle of this page.