This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Standalone Gc Correction Tools

hi, all,
i try to find CNVs from a high-depth resequenced sample (>30x), which is a plant species.
however, several CNV detect tools could only be used for human genomes,
i am wondering if there are some standalone tools that can get gc-corrected read counts using BAM file as inputs.
then we can use call CNVs based on these corrected values.

gc cnv
• 4,328 views • link
updated by Biostar Biostar • written by Plantae Plantae

1 answer

Hi,

Why don't you try CNVnator, it does GC corrected profile analysis using mean shift approach.

Link: CNVnator

• 0 views • link
written by R Ravi • R Ravi

Log in to answer this question.

More posts like this
  • Samtools Depth Option For More Than One Bam Files
    written by Maria333 • Maria333
    <p>Hi everyone,</p> <p>I've been stuck on this for several days. I want to use the <a href='http://samtools.sourceforge.net/'>samtools</a> depth command but not only for a single …
  • Tools For Analyzing Copy Number Variation On All-Tumor Exome-Seq Samples
    written by newDNASeqer newDNASeqer
    <p>My exome-seq data all derived from sequencing tumor samples. I am wondering what's the best tool for detecting CNVs in these samples. From my understanding, …
  • Compute Binned Gc-Normalized Read Counts From Bam File
    written by Christian Christian
    <p>Binned read counts can be readily obtained from <a href='http://samtools.sourceforge.net/SAM1.pdf'>BAM</a> files using for example 'samtools depth' or <a href='https://code.google.com/p/bedtools/'>bedtools</a>. However, I would be interested in …
  • Cnv Analysis On Genes
    written by Adrian Pelin Adrian Pelin
    <p>Hello,</p> <p>Is there a CNV variant caller that works on non-model organisms and that works by providing a <a href='http://samtools.sourceforge.net/SAM1.pdf'>bam</a> alignment, a fasta reference and …
  • Error In Converting Sam To Bam By Samtools
    written by Raghav Raghav
    <p>hello every one,</p> <p>after mapping,i encountered an error during converting my <a href='http://samtools.sourceforge.net/SAM1.pdf'>sam</a> out file into <a href='http://samtools.sourceforge.net/SAM1.pdf'>bam</a> out put file.</p> <p>[cdac@nbri <a href='http://samtools.sourceforge.net/'>samtools</a>-0.1.19]$ <a …
  • Calculate Coverage From Bam File
    written by meredith19 • meredith19
    <p>Is there a way to calculate 5x, 10x, 20x, 30x coverage from a <a href='http://samtools.sourceforge.net/SAM1.pdf'>BAM</a> file ?</p> <p><strong>EDIT:</strong> I have a <a href='http://samtools.sourceforge.net/SAM1.pdf'>BAM</a> file and …
  • Chip-Seq Peak Calling Using Macs For Replicates In Galaxy
    written by anon111 • anon111
    <p>I'm new to Galaxy. I have Chip-seq data for two cell types. Each cell type has two replicates. I already ran an alignment workflow in …
  • How To Prepare The Input File For The Readdepth
    written by luofei.whu • luofei.whu
    <p>Hi I'm trying ReadDepth to call CNV. Anyone knows how to prepare the input Bed file from the <a href='http://samtools.sourceforge.net/SAM1.pdf'>BAM</a> file. There are only short …
  • Fasta File To Sam Conversion
    written by Rallapalli Sukeerthi Teja • Rallapalli Sukeerthi Teja
    <p>Hi,</p> <p>Is it possible to convert a fasta file to <a href='http://samtools.sourceforge.net/SAM1.pdf'>sam</a>/bam format using galaxy OR <a href='http://samtools.sourceforge.net/SAM1.pdf'>Sam</a> tools in MAC ? </p> <p>And how …
  • Svdetect-Structure And Cnv Detection
    written by Hmm • Hmm
    <p>I have patient tumor/normal HiSeq paired end data. I have 2 <a href='http://samtools.sourceforge.net/SAM1.pdf'>bam</a> files which were cleaned/sorted/duplicates removed.One <a href='http://samtools.sourceforge.net/SAM1.pdf'>bam</a> for tumor and other for …