• How to generate the contigs ploidy priors table (yeast) for GATK DetermineGermlineContigPloidy --contig-ploidy-priors option ?

    Hi !

    I was asked to determine the ploidy level and to do **CNV calling** on a **yeast sample** ...

  • Why bcftools gives (Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid)

    I'm using
    Command:

    bcftools call -m -O v /10248_S4_L001_R1_001Sorted.vcf > /10248_S4_L0...

  • Ploidy in copy number analysis

    Hi
    For cancer copy number calling, recently many tools provide integer copy number calls after pr...

  • bcftools for plant SNPs

    Hi, I ran bcftools in the following way:

    bcftools mpileup -O b -o ${3}-${basename}.bcf -f $a...

  • Joint variant calling

    Hi,

    I have 1500 bacterial clean and sorted alignment bam file and I want to call variant and pro...

  • Beagle VCF header issue

    I've received a bed/bim/fam set of data that I'm trying to use for imputation, and I'm having iss...

  • Note: Neither --ploidy nor --ploidy-file given, assuming all sites are diploid [mpileup] 1 samples in 1 input files

    Hello everyone

    i am facing a problem while run a command to call variant, i am using sorted.bam...

  • How to interpret ABSOLUTE plots

    Hi all,
    I am recently trying to use ABSOLUTE to evaluate tumor purity and ploidy. I have some que...

  • PureCN: Tool for estimation of tumor purity and ploidy

    Hi, I'm trying to calculate tumor purity and ploidy using a tool called PureCN written in Rscript...

  • How to handle allosomes and chrM in GATK?

    I'm using whole-genome sequencing (human) data for variant calling using GATK HaplotypeCaller. By...

  • HaplotypeCaller analysis: gVCFs of several plant individuals with various ploidy levels

    Hi  members,

     I've made GATK analysis for 340 plant individuals with various ploidy levels ( 2x ...

  • How to handle hexaploidy of Wheat for vcf file

    I have a GBS data for wheat. I mapped it to reference and then used freebayes for variant calling...

  • Merge contigs in fasta file

    Hello All,

    I am running variant calling on some species whose reference genomes have a very high...

  • Ploidy for variant calling in tumor pooled samples for amplicon next-generation sequencing

    Hello everyone,

    I am trying to call rare variants in pools of four **tumor** samples for a speci...

  • Need help using Shrimp2 on paired end color-space SOLiD data.

    Hi,

    I have SOLiD reads which are paried-end (75bp and 35bp) in .csfasta and .QV.qual format. I w...

  • fitting model to a read coverage spectra

    K-mer spectra of genomic reads are usually modeled as a poisson mixture process where each of the...

  • Contig/Scaffold Length- Variant Calling

    In our lab we have preliminary assembly on non-model genome organism. In the assembled genome, l...

  • PureCN: Tool for estimation of tumor purity and ploidy

    Hi, I'm trying to calculate tumor purity and ploidy using a tool called PureCN written in Rscript...

  • How to filter short length blast results from output

    I'm currently trying to work with a set of plant nucleotide contigs that are all greater than 300...

  • Why bcftools + guess-ploidy is not giving the correct results

    Hi,

    I have used bcftools +guess-ploidy on some of the vcf files but every sample is predicted as...

  • Variant calling and downstream analysis

    Hi,

    I have whole genome sequencing data of 1605 bacterial samples in paired-end reads fastq form...

  • Ploidy in R

    Is there any way I can calculate ploidy for each chromosome in R using bedcov file?

  • gCNVKERNEL Error while using GATK 4.1

    Hi,

    I am trying to run GATK 4.1 on WES data for germline CNV detection, and received an error ab...



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