removed reads that failed vendor QC and their mates

[jorge]

Hello,

I need to remove from a bam file those reads that didn't pass the vendor QC and also their corresponding mate reads.

Has anybody done this?

Any help will appreciated!

Thanks
Jorge

[swbarnes2]

Hello,

I need to remove from a bam file those reads that didn't pass the vendor QC and also their corresponding mate reads.

Has anybody done this?

Any help will appreciated!

Thanks
Jorge

If the software that made the .bam puts the sam flag for failed vendor QC, you can filter the .bam with samtools view.

[jorge]

Hi,

Yes but if one read passed the QC while its mate didn't the flag is only applied to the last one (the one that didn't pass), So If I'm right I that filtering would not remove both reads.

Basically I need to remove both reads even if only one of them didn't pass the QC

Jorge