Skip to main content
10 votes

What is indel calling and what is its purpose?

There are two types of INDELs: short indels and long indels. Some put the threshold at 50bp; others choose 1000bp. Short and long indels are called differently. <50bp short indels are called from ...
user172818's user avatar
  • 6,575
9 votes
Accepted

What is indel calling and what is its purpose?

Insertions and deletions (indels) are one type among many different types of genetic variation, such as single nucleotide variants (SNVs), copy number variants (CNVs), and structural variants (SVs). I'...
Daniel Standage's user avatar
6 votes
Accepted

What is the distribution of indel sizes in a healthy human genome? of insertion:deletion ratios?

One of the 2015 papers from the 1000 genomes project has a nice figure (figure 1) showing the size distribution of medium to large sized insertions and deletions: From another 2015 1000 genomes paper,...
Devon Ryan's user avatar
  • 19.7k
6 votes

How to check if indels in VCF files are left or right aligned?

One possibility is to run bcftools norm on the file. At the end it will print out a statistic about how many variants were realigned. I did this for dbSNPv151 (GRCh38) only for chromosome 22 like this:...
finswimmer's user avatar
  • 1,352
5 votes

How to check if indels in VCF files are left or right aligned?

By definition in the VCF format specification the POS field is left aligned POS int32 t 0-based leftmost coordinate To confirm that you VCF is following the standard you would have to look at the ...
Bioathlete's user avatar
  • 2,584
5 votes
Accepted

After artificially creating events in a FASTA file, how do I keep track of the old coordinates?

I've written a handful of programs from scratch to simulate mutations and variations in real or simulated sequences. The trick has always been to sort the variants by genomic coordinate, apply the ...
Daniel Standage's user avatar
5 votes

What is the distribution of indel sizes in a healthy human genome? of insertion:deletion ratios?

Genome-In-A-Bottle (GIAB; version 3.3.2) contains 3.21M SNPs on auto+X chromosomes and 0.51M INDELs in 2.58Gb confident regions. The ins:del ratio is 0.92. On the CHM1-CHM13 pacbio assembly (European ...
user172818's user avatar
  • 6,575
4 votes

Matches, mismatches and indels

Try one of these: GATK: https://gatk.broadinstitute.org/hc/en-us/articles/360036194592-Getting-started-with-GATK4 freebayes: https://bioinformaticsworkbook.org/dataAnalysis/VariantCalling/freebayes-...
story's user avatar
  • 1,603
4 votes

After artificially creating events in a FASTA file, how do I keep track of the old coordinates?

If you look for a program which would randomly introduce SNPs + short indels and then would save everything into a VCF file, DWGsim or Mason Variator could be a good choice. Then you can create a ...
Karel Břinda's user avatar
4 votes
Accepted

How can I speed up INDEL calling/correction on BAM files?

I wasn't aware of the samtools subsampling when I had this problem a couple of years ago, so ended up writing my own digital normalisation method to deal with mapped reads. This method reduces the ...
gringer's user avatar
  • 14.7k
3 votes
Accepted

Best way to detect long insertions in bisulfite sequencing data?

You'd be best off by starting with -rfg and -rdg as is and reverting bismark's change of ...
Devon Ryan's user avatar
  • 19.7k
2 votes
Accepted

Generate SNP/indel annotation in Arabidopsis

The Ensembl Variant Effect Predictor will annotate your A. thaliana variants: http://plants.ensembl.org/Oryza_sativa/Tools/VEP The web based tool will use the reference genome assembly and gene ...
Ben_Moore's user avatar
  • 146
2 votes

Sort reads in BAM file based on presence of specific deletion?

The CIGAR string should tell you if a read has a deletion in it. So filter the bam files based on that.
swbarnes2's user avatar
  • 1,971
2 votes

How to extract reads with INDELs > a given size?

There's no simple way to do that with awk, since you would need to parse the CIGAR string and iterate over the operations. In python using pysam you would iterate over the reads and filter as follows: ...
Devon Ryan's user avatar
  • 19.7k
2 votes
Accepted

VCF: false insertions?

Microsatellites, minisatellites and other type of repetitive variation are a known feature of genomes. I agree with previous comments in the sense that what you are observing here might as well be ...
JRodrigoF's user avatar
  • 857
1 vote

Can I interpret 15x coverage area as a part of one strand is missing?

UPDATE: Seeing a different question where similar vocabulary is used: it would not be one strand that would be lost. single stranded DNA is not very happy in the nucleus, and would either lead to ...
Maximilian Press's user avatar
1 vote
Accepted

Tree Building Algorithm that treats gaps as deletions

I need to do a more thorough testing to determine just how effective this answer may be, but I think I've put together a workflow that is close enough to an appropriate answer that I'd post it here. ...
CCranney's user avatar
1 vote

A unified database for CNV, SNP, Indel and MSI

To Answer my own question, one can use variation viewer to get all the information :) DisGeNet is another resource.
Angelo's user avatar
  • 237
1 vote
Accepted

Sort reads in BAM file based on presence of specific deletion?

I was asked to write some code sometime near the end of last year to do this, so that viral sequences could be split based on variants at a particular location. The code I wrote doesn't actually do ...
gringer's user avatar
  • 14.7k
1 vote

How can I extract all known mutations of my BAM (or SNP/INDL files)?

If you have a BAM file, you could easily run a variant caller analysis software such as freebayes, though you would need a good amount of computing power like a cluster or a dedicated node with good ...
user8893's user avatar
1 vote

Detection of CNV(InDel) of intermediate size

There is a trade off between read length and the limit of the indel that can be accurately mapped. Intermediate-size indels specifically are better detected with longer read lengths.
Husami's user avatar
  • 11
1 vote

Detection of CNV(InDel) of intermediate size

My impression is that small InDel (a couple of bp) is identified through cigar string in BAM... Well, yes, by gaps in the alignment, easily detected by examining the CIGAR string. ...and typical ...
Daniel Standage's user avatar
1 vote

Find indels between two short sequences

Smith-Waterman is guaranteed to give you the best alignment given your choice of substitution matrix. For a few such tiny sequences, it's what I would use. Many implementations exist.
Edward Kirton's user avatar
1 vote

Store and search on variant and annotation data

The question you linked is about storing genotypes. Your question is about keeping site information, which is different and much easier. As to solutions, you can parse the information you want and ...
user172818's user avatar
  • 6,575
1 vote

Generate SNP/indel annotation in Arabidopsis

I recently used SIFT4G to predict the deleteriousness for a SNP dataset in Arabidopsis. I noticed that besides this, the tool also provides annotation for the SNPs (like gene region, amino acid ...
Duveltje's user avatar
1 vote

Is it possible to use SNP heterozygosity as a proxy for Indel heterozygosity?

SNPs, insertions, and deletions are generated by different biological processes (see for example here). I would expect the per-generation rates of these mutational processes to vary across species. I ...
winni2k's user avatar
  • 2,286

Only top scored, non community-wiki answers of a minimum length are eligible