Tag: mpileup

samtools mpileup error – 1 samples in 1 input files

samtools mpileup error – 1 samples in 1 input files 0 Hi All, I have relatively new to bioinformatics and have encountered an issue when trying to generate an mpileup file with samtools. I have entered the following command samtools mpileup -f /home/path_to_reference/nCoV_Jan31.fa.fasta sorted_sample1.sam > sample.mpileup The message returned is…

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How to call LOH with FreeC

How to call LOH with FreeC 0 Good morning, I am try to infer loss of heterozygosity (LOH) from WGS data using Freec. For this purpose, I am using these parameters in the “[BAF]” section of the configuration file: [BAF] makePileup = My_somaticVCF.vcf.gz fastaFile = hg19.fa SNPfile = hg19_snp142.SingleDiNucl.1based.txt.gz When…

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Removing reads which map to certain region of reference

Removing reads which map to certain region of reference 0 I have mapped reads to a reference genome of a related species. I want to remove reads which map to a specific region (chromosome) of the reference, but I don’t know what the best way to go about it is….

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How to call variant by –max-depth for RNAseq

Hi everyone! I have a query regarding variant calling from a high coverage site on the basis of the maximum likelihood variant. I have RNA-seq data mapped bam file. I called variant using the below command. “bcftools mpileup –max-depth 10000 -Oz -f ref.fa sample.bam | bcftools call -mv -Oz -o…

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Parallel genomic responses to historical climate change and high elevation in East Asian songbirds

Extreme environments present profound physiological stress. The adaptation of closely related species to these environments is likely to invoke congruent genetic responses resulting in similar physiological and/or morphological adaptations, a process termed “parallel evolution” (1). Existing evidence shows that parallel evolution is more common at the phenotypic level than at…

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VCF samtools

VCF samtools 0 Hello, I am having trouble when doing variant calling with samtools. I am getting only the header an no variants. If I would instead use Freebayes, I do get a lot of variables, and with Gatk, I get just a few. What can the problem be? Do…

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Single-cell DNA and RNA sequencing reveals the dynamics of intra-tumor heterogeneity in a colorectal cancer model | BMC Biology

Organoid culture of small intestinal cells and lentiviral transduction C57BL/6J mice and BALB/cAnu/nu immune-deficient nude mice were purchased from CLEA Japan (Tokyo, Japan). The small intestine was harvested from wild-type male C57BL/6J mice at 3–5 weeks of age (Additional file 1: Figure S9A). Crypts were purified and dissociated into single cells,…

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The sardine run in southeastern Africa is a mass migration into an ecological trap

INTRODUCTION Large-scale annual migrations occur in an extraordinary range of animals, from insects to the great whales. While the driving mechanisms of these migrations are varied and sometimes poorly understood, they often represent a way of optimizing conditions for breeding and adult fitness when these are in conflict. Often, populations…

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samtools mpileup fail to create bcf

samtools mpileup fail to create bcf 1 I have indexed my reference.fasta using bowtie2: bowtie2-build reference.fasta reference.fasta created the bam file form the sam file using samtools, sorted and indexed the bam file: samtools view -S -b Sample1_mapped.sam > Sample1_mapped.bam samtools sort Sample1_mapped.bam -o Sample1_sorted > Sample1_sorted.bam samtools index Sample1_sorted.bam…

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phase_trio.sh | searchcode

phase_trio.sh | searchcode PageRenderTime 24ms CodeModel.GetById 16ms app.highlight 5ms RepoModel.GetById 1ms app.codeStats 0ms /Phase/phase_trio.sh github.com/BioinformaticsArchive/fCNV Shell |…

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Bcftools how to add DP to FORMAT field (get per sample read depth for REF vs ALT alleles )

Bcftools how to add DP to FORMAT field (get per sample read depth for REF vs ALT alleles ) 1 I’m trying to achieve what this post was looking for Add Dp Tag To Genotype Field Of Vcf File Currently this is my command: bcftools mpileup -Ou –max-depth 8000 –min-MQ…

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Vcfutils error code

Vcfutils error code 20-08-2021 code at line (I think) just to get it to write a proper fq. Second issue is this error: substr outside of string at /usr/local/bin/object91.ru line We can do this in a single…

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Calling variants on reads with MAPQ=0 on HaplotypeCaller or bcftools mpileup

Calling variants on reads with MAPQ=0 on HaplotypeCaller or bcftools mpileup 2 I am working with about 500 samples of human exome data. used hg19 to align my reads and ran a standard best-practices GATK workflow. Later only to realise that a small 1Mb loci has not mapped properly due…

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EOF marker absent in VCF

EOF marker absent in VCF – can this be safely ignored? 0 Hi, I generated a VCF file using a bcftools mpileup | bcftools call pipeline. I have done this before, and the file produced then looks fine. However, the log for this one had [W::bgzf_read_block] EOF marker is absent….

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bcftools consensus still returns “Could not parse the header” error

bcftools consensus still returns “Could not parse the header” error 0 I attempted to create a consensus fasta file using bcftools, i.e. bgzip -c All_SRR_SNP_Clean.vcf > All_SRR_SNP_Clean.vcf.gz tabix All_SRR_SNP_Clean.vcf.gz cat $ref| bcftools consensus $vcf_dir/All_SRR_SNP_Clean.vcf.gz > consensus.fasta where $ref is the path to a Drosophila reference genome fa and the vcf…

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Extremely low number of variants in VCF file after filtering MIN(FORMAT/DP)>10

Extremely low number of variants in VCF file after filtering MIN(FORMAT/DP)>10 0 I’m doing microbiome analysis where I’m looking for SNPs in a large number of microbe species’ genomes. I ran my bcftools pipeline on around 15 bacterial and viral species from which the end result produced a number of…

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