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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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Identifying somatic mutations in cell lines

I would like to identify the somatic mutations present in a cell line and characterise the genes that are potentially affected by those mutations. For example, are there oncogenes mutated in a ...
Macintosh's user avatar
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3 votes
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Different human reference genomes from NCBI and ENSEMBL, and variant annotation with Variant Effect Predictor (VEP)

Background: I have been working on a human variant calling pipeline, from whole exome reads to variant annotation. For variant annotation I used the Variant Effect predictor (VEP), which is Ensembl ...
Dandelion's user avatar
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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 structural variant [SV] callers) on four WGS samples. The two other callers ...
Dominique M's user avatar
2 votes
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concatenating windowed VCF files, but quickly?

I am calling variants from WGS for a genetically diverse species which, with my sample size, produces a (bgzipped) VCF of around 500G. I am using a nextflow pipeline to chunk up the genome, call ...
nreid's user avatar
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INDELS in PLINK files converted to VCF

I want to compare/validate variants called from sequencing data with array (plink format) variant data. I converted the plink files (.bim, .bed, and .fam files) with plink1 to vcf files. ...
Dandelion's user avatar
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Feasible to find genetic variations of two samples using RNAseq data?

I have bulk RNAseq data from two strains of mice from Jackson Lab: C57BL/6 and B6.SJL. The former expresses a Ptprc-b allele and the latter expresses a ...
geom_na's user avatar
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Difference between pileup and mpileup in VarScan and samtools

I'm going to call variants with VarScan from a pileup files created with samtools. I realized that there are in general two major possibilities to call variants, pileup as well as mpileup. The VarScan ...
Anti's user avatar
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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 ...
gc5's user avatar
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2 votes
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50 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 ...
Sergio.pv's user avatar
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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 ...
Ahmed Abdullah's user avatar
1 vote
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142 views

bwa mem hangs after a few thousand reads

I am trying to align a bunch of paired sample fastq files using bwa mem. My original command was: ...
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Which type of variant caller should I use in a WES normal cell line sample?

I have whole-exome sequencing data of an immortalised non-tumor (normal) cell line that I wish to assess for the presence/absence of APC/Wnt mutations. This is to double check that the cell line is ...
kane9530's user avatar
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Benchmarking for variant identification using RNA-seq data

I am in need to benchmark the variant identification pipeline which uses RNA seq data alone without any matched-normal. I would like to know the reference dataset (and the pipeline on which the ...
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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 ...
Set's user avatar
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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 ...
Adamm's user avatar
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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 ...
unicorn's user avatar
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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 ...
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ERROR IN FUNCOTATOR: [SQLITE_IOERR_LOCK] I/O error in the advisory file locking logic (disk I/O error)

I ran the "funcotator" step from the GATK somatic short variant discovery (snvs + indels) pipeline and used the output of filtermutectcalls as input, but ...
Rita Soares's user avatar
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How deep variant and others preprocessed insertion and deletion for extracting candidate variant?

I am trying to build a model for variant calling,but I am a bit confused how to pre-process the reads that has insertion and deletion and align them with reference? Should I add something to the ...
Ali Akay's user avatar
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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 ...
Scott XU's user avatar
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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 ...
gc5's user avatar
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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 ...
AWE's user avatar
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