Quality format in .bam

[slakov]

Hello,

my question is, how to determine the format of quality scores for bases in .bam format, i.e. is it ASCII-32 or ASCII-64? I know that some files where aligned by bwa with -I flag, some not. So I wonder if somebody knows a quick way to determine if it's 32 or 64 and how to convert .bam files between them.

Many thanks upfront!

[GW_OK]

There's a chart towards the bottom of this page:

http://en.wikipedia.org/wiki/FASTQ_format

Which might help determine what type of quality score it is.

[krobison]

SAM specification states quality as qual+33 encoded; I hope nobody is muddying the waters by writing files otherwise, but it wouldn't shock me.

FASTQ is of course a different story.

[slakov]

SAM specification states quality as qual+33 encoded; I hope nobody is muddying the waters by writing files otherwise, but it wouldn't shock me.

FASTQ is of course a different story.

But what is the flag -I in bwa. Now I afraid that the quality in SAM format is the same but the flag indicates the format of FASTQ qualities, then some quality scores in SAM are wrong, messy...

[nicolallias]

From http://bio-bwa.sourceforge.net/bwa.shtml

-I The input is in the Illumina 1.3+ read format (quality equals ASCII-64).

How wrong, messy ? Could you paste here a short example ?

[ttnguyen]

fastQC can help:

http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/

It runs very fast and you can input fastq, sam or bam.

[slakov]

nice tool, thanks! now I see that the quality format is different. Any fast conversion tools around?