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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Replicating VCF Filtering & Trait-Based SNP Extraction Workflow
I'm new to handling SNP genotyping data in VCF format.
My goal is to identify significant SNPs linked to a specific trait (like "height") for specific samples in a multi-sample VCF file. My ...
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true depth per gvcf location instead of min depth per gvcf block
I am using deepvariant to calls variants on my (WES) data. I am outputting a gvcf file.
I am wondering (I cannot find anything in the documentation) how it would be possible to get the true depth per ...
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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 ...
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How do I quantify a specific somatic variant?
I'm working with targeted Illumina sequencing data generated with DNA from diseased and healthy tissue (this is an age-related disease and is not cancer/neoplastic). My hypothesis is that the diseased ...
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Variants from multiple tools: normalization before or after annotation with VEP?
We want to compare some variant calling tools and their calls on Whole Exome Sequencing data. We will have to normalize the variants that are called (.vcf format) before comparison using for instance ...
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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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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 ...
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How to run a GATK Docker Image with local files?
I'm trying to use the HaplotypeCaller from the GATK toolkit but I keep getting an error. I pulled GATK through Docker and am using this command:
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which SNP effect software, such as VEP, annovar or snpEff, allows the user to submit their own annotations in gtf format?
I have a use case where I want to annotate the variants from running Oxford Nanopore's Medaka on a very simple reference, a single sequence starting on an ATG and finishing on a stop codon (no introns)...
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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.
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Choosing the best number of species for assay
I am doing amplicon sequencing of a virus across many different regions. Lets say I have 20k unique variants of the same virus that I put into my pcr assay and after sequencing and amplifications I am ...
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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 ...
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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 ...
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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 ...
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Getting VCF file that contain common SNPs from 6 VCF file using isec
I have 6 VCF files, where I would like to obtain the SNPs that are common (by position) in all the 6 files. I have tried this command
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