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).

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1answer
18 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-...
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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 ...
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15 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 ...
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22 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 ...
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Pindel has an extremely large output

I am wondering if I am doing something wrong here. I ran Pindel (alongside two other SV callers) on four WGS samples. The two other callers report approximately 50000 SVs and have a decent running ...
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1answer
30 views

No MQ tags in VCF files

To call minority variants in my Mtb sequences I'm using a pipeline of ...
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1answer
24 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 "...
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77 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 ...
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41 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 ...
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1answer
26 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 ...
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250 views

Using BaseRecalibrator in GATK4

GATK4's BaseRecalibrator uses a list of known variants to adjust the base quality scores in a BAM file. I would like to visualize the pre and post recalibration ...
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78 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 ...
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49 views

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

In Strelka vcf in INFO column we have these ...
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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. ...
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53 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 ...
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21 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 ...
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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 ...
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1answer
50 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 ...
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11 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 ...
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3answers
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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 ...
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1answer
78 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: ...
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109 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 ...
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1answer
33 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 ...
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39 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" ...
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219 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 ...
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2answers
116 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 ...
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119 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 ...
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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 ...
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3answers
81 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 ...
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234 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 ...
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1answer
176 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. ...
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646 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 ...
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4answers
556 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 ...
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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). ...
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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), ...
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2answers
768 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 ...
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1answer
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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 ...
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2k 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 ...
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3answers
638 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: ...
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2answers
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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 ...
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544 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 ...
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224 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 ...
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82 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 ...
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1answer
883 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 ...
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169 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 ...
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4k 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 ...
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261 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 ...
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549 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 ...
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280 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 ...
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6k 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 ...