This is a test version of Biostars. For the public version, visit https://www.biostars.org.
What Do You Do With Indels Data?

I have a list of insertion and deletion from a whole genome sequence obtained by next generation sequencer, 

chr, pos and sequence for each indels aligned to our reference genome.

I'm not familiar with this kind of study and the literature didn't give out anything. I was wondering where to start to analyze indels.

Any suggestion is always Welcome :)

indel analysis
• 2,537 views • link
updated by Biostar Biostar • written by User 2005 • User 2005

1 answer

As a start, I'd suggest converting to VCF or a format understood by snpEff, Ensembl Variant Effect Predictor, Bioconductor VariantAnnotation package, or annovar. These programs are useful for determining the effects of small indels on coding genes.

• 0 views • link
written by Sean Davis Sean Davis

Log in to answer this question.

More posts like this
  • Homopolymer sequencing error in IonProton reads
    written by Ashutosh Pandey Ashutosh Pandey
    I am analyzing reads from a mouse genome sequenced using Ionproton machine. Around half of the reads aligned against the reference genome used either an …
  • Bowtie Vs Bwa For Indels
    written by Varun Gupta Varun Gupta
    <p>Hello Everyone</p> <p>I am working on some yeast strains and I am interested in INDELS. The <a href='http://samtools.sourceforge.net/SAM1.pdf'>bam</a> files I have are the ones aligned …
  • Very High Percentage Of Reads Are Pcr Duplicates - Iontorrent
    written by Davy Davy
    <p>Hi All, Recently I have been given some targeted iontorrent sequencing data to play with. It's not large amount of data only ~ 18,000 unpaired …
  • Store Structural Variants Into Vcf
    written by Tomáš Beluský • Tomáš Beluský
    <p>Hi, after <a href='http://www.biostars.org/p/63936/'>question about representing deletion</a>, I've got some more questions about other structural variants in VCF, so I try to put them all …
  • Deciphering Cigar
    written by Leszek Leszek
    <p>Hi, I need to get 5'-end position of each read in <a href='http://samtools.sourceforge.net/SAM1.pdf'>SAM</a> file. For reads aligned in forward direction it's provided in <a href='http://samtools.sourceforge.net/SAM1.pdf'>SAM</a> …
  • How To Interpret Ciend And Cipos Fields In Vcf Files From 1000 Genomes?
    written by agnieszka • agnieszka
    <p>Here is an example variant for genome NA20317. It comes from 1000 genomes data (file: <a href='ftp://ftp.ncbi.nih.gov///1000genomes/ftp/release/20110521/ALL.chr8.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz'>ftp://ftp.ncbi.nih.gov///1000genomes/ftp/release/20110521/ALL.chr8.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz</a>) and was obtained with tabix and vcf-subset script:</p> …
  • Converting Wgsim Output To Vcf
    written by Pascal Pascal
    <p>Hi</p> <p>Since I haven't found any tool that does it I will try to do myself a small script that convert the wgsim output (indels) …
  • Why Does Vcf Aggregate Indels Like This?
    written by Jeremy Leipzig Jeremy Leipzig
    <p>From:</p> <p><a href='http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41'>http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41</a></p> <p><hr/> SNPs and Small Indels</p> <p>For example, suppose we are looking at a locus in the genome:</p> <pre><code>Ref: a t C g …
  • Tool To Find Non Synonymous Snps
    written by Madkitty • Madkitty
    <p>We did a whole genome sequence of our samples and now we have a list of about 20,000 SNPs annotated against refgene (from UCSC). The …
  • Old Blastall Vs New Blastall
    written by User 4143 • User 4143
    <p>I've been using blast 2.2.15 for a while, and I recently downloaded blast 2.2.25 on my new computer. I wanted to test the new version …