Tag: FreeBayes

Bioinformatics Analyst in Minneapolis, MN for University of Minnesota, Twin Cities

Details Posted: 13-Aug-22 Location: Minneapolis, Minnesota Salary: 43944.32 – 123022.07 Categories: Research Support – Laboratory/Non-Laboratory Staff/Administrative Additional Information: 2 openings available. The Research Informatics Solutions (RIS) group within the University of Minnesota Supercomputing Institute (MSI) is hiring two full-time Bioinformatics Analysts to support research at the University of Minnesota. Analysts…

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Freebayes-parallel with large bam file – individual threads running for >6 days

Context: I’m trying to call variants on a sequencing project using pooled genotyping-by-sequencing. Pools consist of 94 samples each, alongside a number of individuals. Sequence data was demultiplexed and then aligned to a reference genome using hisat2, and the resultant bams were merged with samtools merge. The problem bam is…

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snp – 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 look to some calls. I found interesting, homozygous one rs477033 (C/G Ref/Alt) with flag ‘COMMON=0’ and very low MAF. I also…

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[moiexpositoalonsolab/grenepipe] freebayes causes early error about number of threads

Hi Lucas, got a weird one for you. If I change the caller from hapotypecaller to freebayes, I get the error below. It’s doubly strange because it seems to occur well before freebayes would be used in the pipeline. [Sat Dec 11 11:13:02 2021] rule samtools_stats: input: dedup/111D03-1.bam output: qc/samtools-stats/111D03-1.txt…

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Phylogeographic reconstruction of the marbled crayfish origin

Procambarus fallax collections and PCR genotyping Animals were collected from various wild populations (Table S1) in compliance with state and local regulations (Georgia department of natural resources scientific collection permit 115621108, state of Florida collection permits S-19-10 and S-20-04). DNA was isolated from abdominal muscle tissue using SDS-based extraction and precipitation…

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High frequency of an otherwise rare phenotype in a small and isolated tiger population

Significance Small and isolated populations have low genetic variation due to founding bottlenecks and genetic drift. Few empirical studies demonstrate visible phenotypic change associated with drift using genetic data in endangered species. We used genomic analyses of a captive tiger pedigree to identify the genetic basis for a rare trait,…

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Exctracting amino acid substitutions

Exctracting amino acid substitutions 0 Good day, I’m trying to develop a pipeline to determine mutations which are responsible for amino acid changes in genes associated with antibiotic resistance. I have roughly 300 bacrtial isolates. My approach so far has not been fruitful, in short this is what i tried:…

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FreeBayes VCF output with FORMAT unknown

Hey, I am looking for a way to add samples ID names to the FORMAT in my vcf file. I have 10 sorted Bam files. I used Freebayes to create vcf files and my next step is merging all 10 files for VcfSampleCompare. And for that I need to define…

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FreeBayes Error

FreeBayes Error 0 Hi- I am trying to use FreeBayes to identify polymorphic sites and it will not run. It keeps throwing this error “unable to find fasta index entry for GL630349”. Does anyone know what to do in this situation? Thank you Galaxy Coursera FreeBayes Polymorphisms • 16 views…

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VCF Filter On Small Genomes

VCF Filter On Small Genomes 0 Hi guys, I am working on a yeast species (Candida glabrata) NGS data to find any mutations related to drug resistance. I am new in bioinformatics so I am using Galaxy.eu to get use to algorithms. There is literature about some genes that mutations…

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