Re: [Samtools-help] [Samtools-devel] Picard Release 1.34

[Sendu B. <sb...@sa...>]

On 01/11/2010 13:59, Alec Wysoker wrote:
> Picard release 1.34 - SamToFastq.java: Flush output files before
> checking for unpaired mates.
>
> - SamToFastq may now output fastq files per read group if
> OUTPUT_PER_RG (OPRG) is specified.  If OUTPUT_DIR is specified with
> OUTPUT_PER_RG then a file (two if paired end) will be output in
> OUTPUT_DIR per read group named after the platform unit for the read
> group.

I've not used SamToFastq yet, but wondered about it's behaviour:

Does it work given a bam file instead of a sam file?

What happens when the sam file contains a mixture of paired and unpaired
reads for the same read group? Ideally the output would be 3 fastq files
(forward, reverse, unpaired)...

Does it auto-handle '=' in place of reference bases, converting them
back to reference bases in the fastq output?

If it sees an OQ tag, will it output the original quality to the fastq,
or the current quality string?


Cheers,
Sendu.


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