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
1answer
40 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 ...
0
votes
0answers
17 views

why counting the number of cluster of variant allele frequency would be used to estimate heterogeneity

I am fairly new to this field,and right now I am working with variant allele frequency for cancer genome,data is from cbioportal. I have read several articles and they claim mutant allele frequency ...
1
vote
0answers
14 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 ...
0
votes
0answers
47 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 ...
1
vote
1answer
34 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 ...
1
vote
1answer
10 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 ...
2
votes
3answers
358 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 ...
2
votes
1answer
31 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: ...
3
votes
1answer
81 views

Remove variants that do not map to human genome

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 reference genome, ALT alleles that do not ...
3
votes
1answer
27 views

Database for germline copy number variations in cancer

I am interested in looking at germline copy number variations in individuals that are at high risk of developing cancer. Are there any databases where I can look, if a CNV seen in our test case has ...
2
votes
1answer
32 views

Knowing which positions are variants

Let's say I'm sequencing a donor, and I have 20X coverage. And let's say all the reads covering a particular base has the same allele at the position. Then, is that position considered a "variant" ...
-1
votes
1answer
123 views

Parsing .vcf file for this information

I have a .vcf file https://www.dropbox.com/s/8v73nppwg3a1tnd/LP2000109-DNA_A01_vs_LP2000103-DNA_A01.SVannotated.txt?dl=0 with this header ...
1
vote
2answers
90 views

VEP output SIFT_score unclear

We have been experimenting with VEP (Variant Effect Predictor). One of the meta data attributes that we are interested in is the SIFT score, indeed when we apply the dbNSFP plug we get a column ...
4
votes
0answers
85 views

Old versions of the reference genome and dbSNP

For benchmark purposes I’m trying to find an old version of the human reference genome (pre-GRCh37) and a matching version of dbSNP. Unfortunately it appears as though older versions of dbSNP aren’t ...
2
votes
0answers
54 views

How snippy makes MSA-like aligned fasta output from multiple samples?

From the log file it seems snippy doesn't do assembly. It only does mapping: fastq --> SAM --> BAM --> VCF --> consensus_seq/snps But if multiple ...
3
votes
3answers
67 views

Which gene I should select from this qqplot

I have a qqplot of my whole genome sequencing data; A plot is for showing possibly significant driver genes. I tried to read about qqplot though but people only say about the skewedness while I want ...
6
votes
2answers
162 views

How to correctly call a VCF file using damaged DNA? (IonTorrent & FFPE)

EDIT: I am updating this question to make it more specific to my issue. For context - original question prior to edit: How do I obtain a deamination metric when doing the variant calling using the ...
3
votes
1answer
111 views

Output from vcftools missingness

I'm new to data filtering on vcf data and vcftools. I performed variant calling on my dataset, CHR22, homo sapiens. I'd like to remove sites that are missing in more than 5% of individuals. ...
5
votes
6answers
362 views

Identifying Indels from Chromatograms

I have around 100 chromatograms (.ab1 files) from Sanger sequencing a genome at loci believed to have an indel. I'm new to interpreting this kind of data in ...
3
votes
4answers
278 views

How to run same command on multiple files?

Hi im doing Variant calling on fastq files for which i have 4000 fq files and the variant calling are done in different 9 steps. Each step generate different files that are output to next steps. So ...
9
votes
2answers
181 views

calling diploid SNVs from long reads

I'd like to call diploid SNV variants from long-reads data (~80SMRTcells PacBio). I have generated a draft reference genome for an indivudual from a heterozygous (~4%) species (Canu+Haplomerger2). ...
2
votes
1answer
35 views

IonTorrent variant caller failing, lack of ZM: tags in BAM files

I have a lot of IonTorrent sequencing data in BAM format that I want to call variants on, using the IonTorrent variant caller. However, for some of the BAM files (for about 12 samples out of ~150), ...
5
votes
2answers
581 views

No variant found using GATK 4.0 HaplotypeCaller

I am doing variant calling on RNA-seq datasets from wheat which is hexaploid,the binary alignment (BAM) files were created using STAR version 2.6.0c and variant calling was done using GATK 4.0 ...
2
votes
1answer
28 views

GRCm37-designed exon target enrichment, which reference to use?

I have exomes from 24 individual mice. The exomes are the product of Roche's SeqCap EZ HyperCap target enrichment kit. I see that the mouse exome design comes from mm9/NCBI37, the previous major ...
3
votes
1answer
648 views

Increase number of threads for GATK 4.0 HaplotypeCaller

I am using GATK version 4.0, I tried to use multiple threads for calling variants using HaplotypeCaller using following command ...
4
votes
3answers
445 views

Issues performing variant calling with GATK

I am trying to perform variant calling on a BAM file generated through STAR version STAR_2.6.0b for wheat genome using GATK haplotypecaller as follows: ...
5
votes
2answers
2k views

Why Ti/Tv ratio?

I'm interested in the transition/transversion (Ti/Tv) ratio: In substitution mutations, transitions are defined as the interchange of the purine-based A↔G or pryimidine-based C↔T. Transversions are ...
4
votes
2answers
343 views

GATK CombineVariants complains the contig order in the VCF files

I have called variants on two strains of C. elegans separately. I now want to merge the VCF files into one using the following code: Create a sequence dictionary of the reference sequence Sort the ...
4
votes
1answer
181 views

Keep Format and Individual fields when annotating VCF with VEP

I'm currently updating my Variant Calling Pipeline by switching the VCF annotating software from Annovar to VEP for a variety of regions, not least how easy it is to annotate with HGVS notation and ...
3
votes
1answer
80 views

Human SNP databases other than dbSNP

I'm working on a project to identify variants as being either germline or somatic based on nearby SNPs, and I was wondering if there were any databases of SNPs for Homo sapiens other than dbSNP? I'm ...
6
votes
1answer
626 views

Merge 2 VCFs from different variant callers

I am working with WES data for detection of somatic variants and I have used two variant callers because no variant caller is complete in itself. I have used GATK Haplotypecaller for small variants ...
6
votes
2answers
152 views

Why chose CNN for a variant caller

Google released their variant caller DeepVariant which won the highest SNP performance award in the Precision FDA Truth challenge (99.999% accuracy). From the linked github repo, we see that ...
7
votes
2answers
3k views

Converting a BAM file into VCF

I have NGS illumina RNA-seq reads from M. musculus (mm10). I am trying to find variants along the strand portion of the reads in the refseq (mm10). I mapped a pair of sequence files and generated a ...
5
votes
2answers
192 views

Books on bioinformatics algorithms

I'm looking for a book about bioinformatics algorithms, such as alignment, BLAST search, and variant calling. I'm hoping reading about this subject will give me a deeper understanding of the ...
2
votes
1answer
474 views

Can I pilon-polish long reads with Illumina short reads to improve structural variant detection?

I have pacbio Sequel data at 50 x coverage for a strain of animal. I would like to find structural variants compared to the reference genome sequence. At the moment, I align my reads to the reference ...
5
votes
1answer
210 views

Can a data file in VCF format be converted into FASTA?

I'm considering purchasing the 'MyGenome' product by Veritas Genetics to analyze my genome for a project. I'd like the data to be in FASTA format, but Veritas only provides VCF data. Is it possible to ...
2
votes
2answers
4k views

How to subset samples from a VCF file?

I have VCF files (SNPs & indels) for WGS on 100 samples, but I want to only use a specific subset of 10 of the samples. Is there a relatively easy way to pull out only the 10 samples, while still ...
5
votes
2answers
2k views

Tools to do VCF to MAF and MAF to VCF conversion?

Normally, I would use the vcf2maf scripts to convert a VCF to a MAF (or vice versa). This is great software, but on my system, perl scripts with dependencies are easy to break. (Here it uses VEP.) ...
0
votes
0answers
84 views

How to install and use pbhoney on Mac OSX?

I download the PBSuite from SourceForge. I decompressed the file. I then moved to this directory: PBSuite_15.8.24/pbsuite/honey and typed: ...
5
votes
2answers
1k views

How can I count the number of reads that support a variant in a bam file?

I am calling variants from a human sample using bwa mem to align the reads and gatk to call the variants. I'm trying to understand why a specific variant was not called in my sample. I have checked ...
1
vote
0answers
96 views

Can Mauve export indels or is there an whole-genome aligner that can export indels?

I have aligned two whole genomes of the same species in Mauve using progressiveMauve. One of the genomes is 2 megabases longer than the other so I know it must contain some insertions. Looking at the ...
4
votes
1answer
172 views

Where can I get the population allele frequency vcf file?

I want to use GATK to estimate cross-sample contamination for Whole Genome Sequencing data. The specific tool is ContEst and it is run with: ...
2
votes
1answer
125 views

What does “motif 2 bp or longer” mean?

I'm reading a preprint on a new somatic variant discovery tool, and the first sentence of the Discussion section has me confused. Across the four datasets analyzed in this study, we discovered that ...
5
votes
3answers
770 views

Somatic tumor only variant calling?

I'm evaluating possibilites for somatic tumor variant calling without paired-normal samples. I'm aware of the consequences without a normal sample. All the popular variant calling tools such as ...
6
votes
2answers
487 views

What is indel calling and what is its purpose?

I'm having a difficulty in grasping the general purpose and concept of indel calling. What exactly is this process?
5
votes
1answer
348 views

Tool or script to parse annotated VCF files

I've annotated VCF files using snpEff and looking for a tool or script to parse the VCF file and clean up the file to make it interpretable for a biologist.
8
votes
3answers
673 views

Selecting sites from VCF which have an alt AD > 10

I have high-depth variant calling created using the HaplotypeCaller with --output_mode EMIT_ALL_SITES I'm interested in finding all sites (regardless of genotype ...
4
votes
2answers
371 views

Why are there missing calls in a VCF file from exome sequencing?

My data is a VCF file generated from an exome sequencing variant call pipeline. I'm not very familiar with the sequencing and variant calling process. I noticed that there are some missing genotypes, ...
5
votes
1answer
776 views

How do I generate a variant list (i.e. VCF file) using Illumina reads from a human genome?

This is a problem I have to solve frequently, and I'd be interested in knowing what other methods people use to solve the same problem. About twice a year, I get asked to determine variants from ...
7
votes
2answers
202 views

How to detect a mutation and predict its consequence?

I read a lecture notes about mutations, what kind of algorithms are there to detect mutations? How do people know if the gene is mutated or whether it's a sequencing error? I saw this which is ...