I don't know the exact number that mapped and are not just in the header but I am sure that many are missing from the pileup file. I used the CLC Genomics software to conduct the mapping and then also called high quality SNPs using the CLC. Many of the contigs that contained high quality SNPs as detected from CLC did not end up in my pileup file but are of course in the SAM file and had good quality.
Thanks Patricia Klein Associate Professor Texas AgriLife Research and Texas A&M University Sent from my iPad > On Nov 7, 2014, at 7:15 PM, Joseph Fass <joseph.f...@gmail.com> wrote: > > 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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