Questions tagged [variant-calling]

The process of discovering variants in individuals starting from sequencing reads. Can be subdivided into germline variant calling and somatic variant calling. Can also be used for the more specific process of finding variants starting with reads aligned to a reference genome (SAM/BAM files).

Filter by
Sorted by
Tagged with
0 votes
1 answer
25 views

Reference variant detected as altered one in bam file

I received (from manufacturer) several .bam files and I used four callers (samtools, freebayes, haplotypecaller, deepvariant) to find some sequence variants. In obtained .vcf files, I took a closer ...
user avatar
  • 162
0 votes
0 answers
42 views

What is the best tools to find all the somatic mutations?

I am a beginner in this field. I would like to know which is the best way to get all the mutations from a certain sample. At this point, I am considering using GATK (here) and Maftools (here). I don't ...
user avatar
  • 135
3 votes
2 answers
52 views

Detect mutation context in a read of a sam file

After sequencing (Illumina) of some DNA, I generated a sam file through alignment of a fastq file (using Bowtie2). Instead of using variant calling programs, I want to know the specific variances, ...
user avatar
0 votes
1 answer
21 views

Range of values for VAF in heterozygous genotype

(VAF = variant allele frequency) This question follows from this one. What is the expected range of values for VAF of mutations with heterozygous genotype (i.e., 0/1 or 0|1)? Is it possible to have 0% ...
user avatar
  • 1,713
2 votes
0 answers
70 views

Assess ploidy estimation through SNV and CNV results

I want to assess ploidy estimation (i.e., diploid vs tetraploid) in a set of samples for which I have both results from the variant caller (i.e., SNVs) and from the copy number caller. What are the ...
user avatar
  • 1,713
1 vote
1 answer
70 views

GATK variant filtration using "SelectVariants" and use of JEXL queries

How to do variants selection in some corner cases using GATK and JEXL expressions? I am following the guidelines given in this links for variant selection for some specific cases are not as much ...
user avatar
0 votes
0 answers
21 views

When can we have duplicated variants in a VCF file, excluding artifacts?

I read these two questions on duplicated VCF variants: 1, 2. However, it is not entirely clear to me when duplicated variants can arise (excluding merging artifacts). I want to understand if ...
user avatar
  • 1,713
2 votes
2 answers
64 views

Nanopore variant calling

So far I haven't done any variant calling as such. Nanopore I have used for 16s microbiome data. Now My question/doubt so how do I proceed for nano-pore virus sequencing data Steps: I get fast5 files ...
user avatar
  • 1,538
1 vote
1 answer
60 views

Meaning of order of alleles in VCF GT field for unphased genotypes

Order of alleles in genotype field (on VCFs) can be used to infer haplotypes However, what about unphased genotypes? I have a VCF file where I only have unphased genotypes: ...
user avatar
  • 1,713
0 votes
1 answer
57 views

Convert VCF file to mpileup.txt

I am working on an iterative analysis that uses orthologous pipelines that require mpileup.txt files as input for a visualization step. This requires me to convert VCF files to mpileup.txt. This ...
user avatar
1 vote
2 answers
225 views

How do I call variants using BCFTools without piping mpileup file?

I need to call variants on a large number of reads using both VarScan2 and BCFTools. Both of these variant calling tools use <...
user avatar
  • 123
0 votes
0 answers
31 views

Fastest way to count where two bam files are homozygote reference (inverted variant calling)

Maybe I'm having a brain-freeze so excuse me if this is a waste of everyone's time... I am working with an organism with ~700Mb genome. I have bam files of two individuals that are whole genome ...
user avatar
  • 121
8 votes
4 answers
948 views

Are variant calling files personally identifiable information?

This question is to be read in the context of data protection. It seems to be common understanding that the whole genome sequence of an individual is personally identifiable, non-anonymizable ...
user avatar
  • 182
2 votes
1 answer
86 views

Consensus sequence from vcf file

I am generating a consensus sequence for SARS-Cov-2. I am visually inspecting every candidate SNP in a pileup. Sometimes I find that there are two consistent variants for the same position, but I can ...
user avatar
2 votes
1 answer
49 views

Detecting SARS-CoV-2 variants from the mixed virus population

I have a fastq file from Nanopore sequencing data that contains reads from both the UK and South Africa variants of SARS-CoV-2. The variants are identified by three key mutations in the receptor-...
user avatar
  • 709
1 vote
2 answers
55 views

Solutions to reference bias issue

I've recently learned about the reference bias issue - inability to properly map NGS reads in certain genomic regions caused by the fact that our standard genomic references are linear and do not ...
user avatar
  • 111
3 votes
2 answers
51 views

Calling for one specific SNP from multiple sequencing runs

Just learning the basics of bioinformatics and bash shell scripting. Is there a correct way to search for a specific allele with one or even multiple sequencing runs? I am searching for prevalence of ...
user avatar
  • 31
1 vote
2 answers
458 views

Can an alternate allele be more common than a reference allele?

I'm trying to analyze data from a genotype-phenotype association study. The genotype data is stored in csv files that record for each variant site and each subject, the alleles that the subject has at ...
user avatar
  • 13
1 vote
0 answers
45 views

SnpEff not correctly annotating multiple-nucleotide polymorphisms

I have some SARS-CoV-2 sequencing data that I'm trying to annotate with SnpEff, however SnpEff doesn't appear to be recognizing multiple adjacent SNPs within the same codon and correctly calling them ...
user avatar
  • 249
1 vote
1 answer
109 views

Why is there no GT-entry in my .vcf file from bacteria

I mapped raw reads obtained from an E. coli genome (.fastq file) to my reference genome. Next, I exported the .vcf (variant calling file), which looks something like the header example shown below (...
user avatar
1 vote
1 answer
137 views

genotyping or variant calling in R

Are there any good options for calling variants or even just a pileup from R? R is not ideal for this, but I'd like to integrate with other functions. I found deepSNV::bam2R which roughly does what I ...
user avatar
  • 2,099
0 votes
1 answer
72 views

Supplementary aligments in VAF

This question has also been asked on Biostars I have a doubt, are supplementary alignment usually considered when the variant allele frequency is calculated? Thanks a lot. In my case I have some ...
user avatar
2 votes
1 answer
88 views

Are there open-sourced graph-based variant callers?

I would like to compare GATK with graph-based variant callers. I have seen the Fast and accurate genomic analyses using genome graphs paper from SevenBridges and the paragraph tool by Illumina, though ...
user avatar
  • 1,347
1 vote
2 answers
75 views

Finding SNP/Indel Markers of Interspecific Variation

This is a revised version of my original question, edited to include the portions already answered by @Maximilian Press. Goal: Find SNP and indel alleles which are fixed between but lack polymorphism ...
user avatar
2 votes
0 answers
33 views

Joint variant calling of two sample sets with different coverages (~5x vs ~25x)

Let's say 50 samples were sequenced at 25x. After a while, the group realizes that the experiment is under-powered and adds 100 samples more, but at a coverage of 5x. I'm talking about WGS. The ...
user avatar
  • 121
1 vote
0 answers
36 views

Calling variants with DeepVariant on targeted NGS sequencing (custom library)

I am seeking advice regarding DeepVariant analysis. To avoid false positives I'm using several variant callers and then the resulting common set will be considered as TP variants. One of the callers ...
user avatar
  • 162
1 vote
2 answers
94 views

How can I get or create a reference genome for Bacteria?

I am a computer engineer and nowadays trying to grasp some concepts of Bioinformatics particularly, reference genomes and genomic variants. My aim is to find the effect of sequence features on variant ...
user avatar
  • 13
3 votes
2 answers
486 views

How does DeepVariant construct RGB images from DNA sequences?

DeepVariant is a pipeline to call genetic variants from DNA sequencing data. A major step, before feeding the CNN, is to translate these DNA sequences into images. It's unclear why and how Google ...
user avatar
  • 1,347
0 votes
1 answer
844 views

Download or create VCF from Human Genome Diversity Project (HGDP)

I can't seem to find HGDP data in VCF format. Does anyone know where I can download it from? Perhaps there a Snakemake pipeline for calling VCFs from this data?
user avatar
0 votes
1 answer
29 views

Non-exome variants called from whole-exome sequencing data

I'm working on rather standard whole-exome sequencing data and treat it the same as whole-genome sequencing data (aligning it to the full GRCh38 reference assembly and calling variants with no exome-...
user avatar
  • 3
0 votes
1 answer
96 views

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

I am using a Genome Explorer tool to see all the mutations on my own DNA. My particular interest is on listing the variants and get their names/ids. Here are a few screenshots: You can see that ...
user avatar
  • 123
0 votes
1 answer
32 views

Best practice to perform a functional analysis on a set of VCFs from a cohort of patients

I am confused about how to perform a functional analysis after a variant calling on a cohort of patients. I have anotated all vcfs and filter them in order to get only those deleterious variants. I ...
user avatar
  • 135
1 vote
3 answers
270 views

Filtering VEP annotation file

I am filtering a VEP annotated vcf, trying to maintain just those variants classified as deleterious by SIFTand as damaging (probably or possibly included) by ...
user avatar
  • 135
2 votes
0 answers
54 views

Pindel has an extremely large output

I am wondering if I am doing something wrong here. I ran Pindel (alongside two other structural variant [SV] callers) on four WGS samples. The two other callers ...
user avatar
1 vote
1 answer
200 views

No MQ tags in VCF files

To call minority variants in my Mtb sequences I'm using a pipeline of ...
user avatar
  • 140
1 vote
1 answer
25 views

How can I find the position of every mutation where the Allele Frequency is greater than X, in regards to a reference such as Hg19?

I have a Human genome sequenced in a BAM file (along with other files with the indels, snps, cnvs). I want to find every mutation with regards to the reference Human genome. However the majority of "...
user avatar
  • 123
0 votes
1 answer
301 views

What samples can be used for a Mutect2 Panel of Normals

I'm working on calling somatic variants from solid tissue tumors. I have one normal and one tumor sample for each patient. I plan to use Mutect2 to call somatic variants after preprocessing the data ...
user avatar
0 votes
2 answers
56 views

Variant calling for a subset of genes using whole gneome sequencing data

I have few 100 raw fastq files from whole-genome sequencing data and I would like to map these files to a set of genes only (and not whole genome) so as to find SNP's associated with them. Can anyone ...
user avatar
2 votes
2 answers
62 views

Detection of CNV(InDel) of intermediate size

My impression is that small InDel (a couple of bp) is identified through cigar string in BAM and typical CNV (at least thousands of bp) is detected through read depth. What about InDel or CNV with ...
user avatar
  • 191
0 votes
1 answer
254 views

Interpreting MultiQC plot of GATK BaseRecalibration data?

I'm using GATK4 to build a somatic variant calling pipeline. The pipeline uses MultiQC to aggregate quality control data, and one of the QC measures reported is base quality score recalibration from ...
user avatar
1 vote
1 answer
101 views

Help with the definitions of fields in a VCF output by Strelka

In Strelka vcf in INFO column we have these ...
user avatar
  • 1,521
2 votes
0 answers
46 views

NA12878 equivalent for somatic variant calling [duplicate]

I'm building a somatic variant calling pipeline with snakemake. The pipeline is hosted on Github, and I'd like to use Travis CI for continuous integration testing. ...
user avatar
0 votes
2 answers
63 views

Questions regarding the detection of variants (SNPs and Indels) in mammal

Greetings, I’m a newbie in bioinformatics working currently on my first project regarding detection of variants (SNPs and Indels) in mammal assembly genome. I used the following method to detect ...
user avatar
1 vote
0 answers
24 views

Effect size in power analysis when dealing with Poisson based variant caller

I was trying to estimate the minimum sequencing depth required to confidently detect somatic variant using Poisson distribution based variant caller (such as somatic variant caller or Pisces from ...
user avatar
  • 191
0 votes
1 answer
134 views

How should I deal with segmental duplications when aligning NGS reads to a reference genome?

This is a follow-up of my other question. I have been having trouble calling variants in the human SMN1 and SMN2 genes, because the human genome has a large segmental duplication there and these two ...
user avatar
  • 7,957
1 vote
1 answer
88 views

swap genotypes for specific fields of a vcf file

Is there a tool already established to "swap" the ref/alt information in the GT, AD and PL ...
user avatar
  • 2,614
1 vote
1 answer
16 views

SnpEff gene annotation with @ such as PCDHB@

I'm using snpEff to annotate some VCFs and getting some spurious annotations that don't have transcript ids. Some of these annotations have a gene name followed by ampersand such as PCDHB@ and I'm not ...
user avatar
  • 195
3 votes
3 answers
3k views

Find overlap between VCF files

I have two VCF files and I want to compare the missing rate in each of them, but I want to only look at sites that are present in both files. How could I go about getting a list of positions that are ...
user avatar
  • 445
2 votes
1 answer
95 views

Why does IGV turn a VCF QUAL of "." into -10?

IGV is turning QUAL "." into -10 from this VCF of structural variations. I'm wondering if this means anything or if I should report a bug to the IGV devs. Here's a row from a VCF: ...
user avatar
  • 195
4 votes
1 answer
142 views

Remove variants that do not map to human genome

[This question was also asked on Biostars] I received an hg38 VCF file that's had variants imputed with 1000 genomes. I've encountered some issues with the VCF; REF alleles that do not align to a ...
user avatar