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 ...
- 6,295
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'...
- 5,010
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,...
- 19.5k
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:...
- 1,332
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 ...
- 2,574
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 ...
- 5,010
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 ...
- 6,295
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-...
- 1,568
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 ...
- 1,899
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 ...
- 13k
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 ...
- 19.5k
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 ...
- 91
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.
- 1,812
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:
...
- 19.5k
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 ...
- 705
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.
...
- 51
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.
- 175
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 ...
- 13k
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 ...
- 11
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.
- 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 ...
- 5,010
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.
- 106
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 ...
- 6,295
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 ...
- 11
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 ...
- 2,166
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