Hello,
I have been unable to extract depth 'DP' info from my vcf files (generated with latest bcftools variant calling (SNPs)) after being converted...
27 results in 0.0030 seconds.
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R, vcfr, extrcat.gt, bcftools filter
Last edited by wbsimey; 08-19-2021, 09:11 AM. -
Discrepancy between samtools IDXSTATS and depth
Hi all,
i am baffled from some results and i was wondering if anyone can help.
I am doing RNAseq.
I got my sample,... -
ATAC-seq library sequencing
Hi,
I am about to submit my first mouse ATAC-seq libraries for sequencing, but I have doubts regarding the number of libraries to pool... -
Pol III chip-seq experimental design
hi all,
we are planning on doing a ChIP-Seq experiment trying to identify PolIII binding sites in yeast and mouse.
As I am not really sure... -
Minimum (ir maximum) bam depth/coverage for structural variation analyses
*or maximum
We are studying structural variation in several plant genomes Illmumina pair-end DNA re-sequencing, and noticed that the number... -
vaxherra started a topic Metagenomic survey of gut microbiota - depth, tradeoff and num. of samples to includein MetagenomicsMetagenomic survey of gut microbiota - depth, tradeoff and num. of samples to include
Hi there community!
I am a student currently enrolled in a Research Traineeship Program. My lab studies Systemic Lupus Erythematosus (SLE),... -
Read depth differs between bcftools and bam-readcount
We are analyzing bam files using bam-readcount and bcftools + mpileup, and comparing the reported level of coverage at specific sites in the genome. We... -
Pooling across lanes and depth
Hi All,
I'm sequencing ~36 metagenomes and I'm thinking about how to get the best coverage.
The easiest thing would be to pool all...Last edited by darthsequencer; 04-24-2016, 02:33 PM. -
CNV by read_depth approach
Hey guys !
I'm actually working on a CNV project for the first time and need your help.
I mapped on a ref genome 44 Ilumina... -
Samtools Depth - Filling in the gaps with 0 - Perl?
Hi everyone,
I thought that perhaps others have encountered and previously solved the following problem:
Samtools depth allows you... -
Samtools Depth
Hey Guys,
I have just installed samtools on the command line and am messing around with the features. One thing I am curious about is deletion... -
Strange strand bias and unusual depths
Hi all,
I'm seeing some very strange stuff with a resequenced prokaryotic genome coming from an Illumina HiSeq 2000. The design is 50bp... -
Identifying a good SNP on IGV
I start working with IGV, but I have some doubts in how to identify a good SPN in this program. First I download the new Soybean Genome on Phytozome (Gmax_275_v2.0.fa... -
VCFtools filtering problem
I'm having some issues filtering individuals out with a GQ below a given threshold.
Using the command ./vcftools --vcf AST.txt --minGQ... -
Power calculation question
I want to compute the power to detect any copy number variant in the genome that is ~100bp, given that I have ~0.5x depth (coverage) of the genome. I...
