Hot answers tagged

10

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 read alignment directly. Modern indel callers essentially build a multi-alignment of reads and call an indel with enough read supports. Short indels may break ...


9

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'll assume here that you know how indels are defined, but are simple trying to understand the importance of discovering and analyzing them. The goal of indel ...


6

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, one can see that the absolute number of smaller indels is much larger, though an exact size range isn't given (as far as I saw). If you really want to know ...


6

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: $ bcftools view -i 'TYPE="indel"' dbSNP_GRCh38.p7_b151.vcf.gz 22|bcftools norm -Ou -f GRCh38.fa > /dev/null Lines total/split/realigned/skipped: 901503/...


5

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 ancestry), there are 3.57M auto+X SNPs and 0.58M INDELs in 2.71Gb confident regions [reference] with an ins:del ratio 0.99. These give you an idea of relative ...


5

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 reference and the match up the entries in the VCF. However if it is from a reliable source like dbSNP you can probably assume they follow the spec


5

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 variant with the largest coordinate first, then apply the variant with the second largest coordinate, all the way down to the variant with the smallest coordinate....


4

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 corresponding Chain file using bcftools consensus -c and transform various formats between these two coordinate systems using CrossMap.


4

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 genome coverage, but preserves reads where coverage is low. Because I was working with IonTorrent reads (which have variable length), I came up with the idea of ...


3

You'd be best off by starting with -rfg and -rdg as is and reverting bismark's change of --score-min back to the default for bowtie2. That alone will allow for much longer indels. If that still doesn't suffice, then I'd play around more with --score-min before messing with the gap open/extend penalties. If you do need to play with those, then increase the ...


2

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 annotation used in the Ensembl browser: http://plants.ensembl.org/Arabidopsis_thaliana/Info/Annotation/#assembly However, if you use the command-line version of VEP,...


2

The CIGAR string should tell you if a read has a deletion in it. So filter the bam files based on that.


2

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: keep = False for OP, LEN in b.cigartuples: if OP == 2 and LEN > 20: keep = True break if keep: ...do stuff...


1

To Answer my own question, one can use variation viewer to get all the information :) DisGeNet is another resource.


1

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 the splitting - it creates SAM read groups based on those variants - but that splitting can be done after processing with this script using samtools split. As ...


1

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 memory. Freebayes outputs a vcf file that has all the variants listed. Then you can load it into the UCSC or Ensembl human genome browsers and look at what genes ...


1

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.


1

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 CNV (at least thousands of bp) is detected through read depth. Also by deviations from expected read pair distance or orientation. What about InDel or CNV ...


1

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.


1

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 store them in a standard SQL database. You can use UCSC binning for region queries. Modern SQL databases all provide R-tree indices, which can be adapted for ...


1

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 substitution, start/stop etc.) They have an Arabidopsis database readily available so you don't have to generate your own. Your input should be enough to run the ...


1

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 would also expect the degree to which each mutational process varies across species to vary as well. I think the answer to your question is "probably not ...


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