Hi !
I was asked to determine the ploidy level and to do **CNV calling** on a **yeast sample** ...
I'm using
Command:
bcftools call -m -O v /10248_S4_L001_R1_001Sorted.vcf > /10248_S4_L0...
Hi
For cancer copy number calling, recently many tools provide integer copy number calls after pr...
Hi, I ran bcftools in the following way:
bcftools mpileup -O b -o ${3}-${basename}.bcf -f $a...
Hi,
I have 1500 bacterial clean and sorted alignment bam file and I want to call variant and pro...
I've received a bed/bim/fam set of data that I'm trying to use for imputation, and I'm having iss...
Hello everyone
i am facing a problem while run a command to call variant, i am using sorted.bam...
Hi all,
I am recently trying to use ABSOLUTE to evaluate tumor purity and ploidy. I have some que...
Hi, I'm trying to calculate tumor purity and ploidy using a tool called PureCN written in Rscript...
I'm using whole-genome sequencing (human) data for variant calling using GATK HaplotypeCaller. By...
Hi members,
I've made GATK analysis for 340 plant individuals with various ploidy levels ( 2x ...
I have a GBS data for wheat. I mapped it to reference and then used freebayes for variant calling...
Hello All,
I am running variant calling on some species whose reference genomes have a very high...
Hello everyone,
I am trying to call rare variants in pools of four **tumor** samples for a speci...
Hi,
I have SOLiD reads which are paried-end (75bp and 35bp) in .csfasta and .QV.qual format. I w...
K-mer spectra of genomic reads are usually modeled as a poisson mixture process where each of the...
In our lab we have preliminary assembly on non-model genome organism. In the assembled genome, l...
Hi, I'm trying to calculate tumor purity and ploidy using a tool called PureCN written in Rscript...
I'm currently trying to work with a set of plant nucleotide contigs that are all greater than 300...
Hi,
I have used bcftools +guess-ploidy on some of the vcf files but every sample is predicted as...
Hi,
I have whole genome sequencing data of 1605 bacterial samples in paired-end reads fastq form...
Is there any way I can calculate ploidy for each chromosome in R using bedcov file?
Hi,
I am trying to run GATK 4.1 on WES data for germline CNV detection, and received an error ab...