To what extent are all 91k contained in your SAM file? Are some just in the header, but there are no alignments to them? The other explanation could be that those contigs have repetitive sequence in them, and all the reads that map to them have zero mapping quality. Those reads will be omitted from mpileup output. ~Joe
On Fri, Nov 7, 2014 at 3:15 PM, Trish Klein <pkl...@tamu.edu> wrote: > I am working with a genome that hasn’t been sequenced but we do have some > de novo assembled contigs to use as a “reference genome” for mapping reads > against. I have ~91,000 contigs in this “reference genome”. After mapping > reads to this “reference genome” I want to then run variant calling using > mpileup. The issue that I see is that my pileup file doesn’t contain the > SNP information for all 91,000 contigs contained in my SAM file. Can > anyone tell me why this might be happening? Much of the data from the SAM > file just doesn’t make it into the pileup file and I don’t know if it is > because I have so many contigs in my “reference genome”. Any help would be > greatly appreciated. > > > > Thanks > > > > Patricia Klein > > Associate Professor > > Institute for Plant Genomics and Biotechnology and Department of > Horticulture > > TAMU2123 > > Texas AgriLife Research > > Texas A&M University > > College Station, TX 77843-2123 > > > > > > > ------------------------------------------------------------------------------ > > _______________________________________________ > Samtools-help mailing list > Samtools-help@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/samtools-help > > -- Joseph Fass Lead Data Analyst UC Davis Genome Center - Bioinformatics Core http://bioinformatics.ucdavis.edu/ jnf...@ucdavis.edu phone ~ 530.752.2698
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