Hi, I¹d like to remove reads with a quality less than 20. My input is Illumina 2500 pair-end WGS 180Mb genome size.
My provisional command is: Samtools view -bS -q 20 input.sam output.bam Does this seem correct, or will the read removal with samtools do something like interfering with read pairs? In some examples I¹ve seen the fastq files used in addition to the input sam file.. My order of operations is: Remove adaptors with ea-utils, Map with BWA mem, Remove bad reads with samtools view, Re-map with Stampy, then use Picard to remove unmapped and duplicate reads, add read group information, and then index, then use GATK to realign around indels. I¹m going to try this out now anyway - just I¹m hesitant on interpreting the output of something that I don¹t understand the input of. Cheers, Will ________________________________________ Research Fellow School of Life Sciences University of Sussex, United Kingdom Tel +44(0)1273 678 559 FAX +44(0)1273 877586 URL http://www.sussex.ac.uk/lifesci/morrowlab/people <http://www.sussex.ac.uk/lifesci/ebe/people/list/person/299309> ------------------------------------------------------------------------------ One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
