Re: [Samtools-help] How to really fix a BAM file?

[Christian C. <C....@du...>]

Hi Karl,

THat's not really what I'm after. I'm look for something to filter a BAM
file not fastq. I have already checked the reads and aligned them to a
genome.

Thanks for your email, though.
Cheers,

Chris



On 24/01/2013 10:50, "Karl Holm" <kar...@eb...> wrote:

>Hi Christian,
>
>
>I usually use a tool like Trimmomatic
>(http://www.usadellab.org/cms/index.php?page=trimmomatic) for cleaning,
>adapter- and low quality trimming as soon as get my fastq files. The
>program
> can be told to output proper pairs in one file and unpaired reads in
>another. If the unpaired reads are many enough I proceed with them
>separately through the pipe and merge with the paired set at a later step
>if appropriate. These days though, I have noticed
> that they are usually very few and of very bad quality so I just discard
>them. I would guess there are several ways to deal with this and mine
>might not at all be the best.
>
>
>Let me know if you find out something better.
>
>
>Cheers,
>Karl
>
>___________________________
>Karl Holm
>Dept. of Ecology and Genetics
>Evolutionary Biology Centre (EBC)
>Uppsala University
>Norbyvägen 18D
>SE-752 36 Uppsala
>Sweden
>
>Tel +46 (0) 18 471 64 10
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>
>On 24 Jan 2013, at 11:18, Christian Cole <C....@du...> wrote:
>
>
>Hi,
>
>I have a BAM file that is failing in GATK and the problem seems to be
>missing mates in the PE reads presumably due to on-target read selection
>step. ValidateSamFile confirms this, but FixMateInformation doesn't fix it
>- what does it actually do?
>
>What tool do I use to remove these unpaired reads that are blocking my
>analysis?
>Cheers,
>
>Chris
>
>
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