I was hoping to get some advice on working with the AD field for variants in VCFs produced by Pindel and Pindel2VCF.
My lab has a variant...
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Pindel and GATK AD Concordance
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Difference between coverage, depth of coverage and targeted coverage
Hi everybody,
I have a question about coverage, depth of coverage and targeted coverage.
What is the difference between those three?... -
Evaluate coverage of specific motifs
Is there a method out there that would allow me to determine whether a particular sequence motif (DNA) has adequate sequencing depth of coverage across... -
Understanding DPF from VCF file
I have VCF file version:, ##fileformat=VCFv4.1 from isaac variant caller.
Header of the output:
#CHROM POS ID REF ALT QUAL FILTER...Last edited by bio_informatics; 09-26-2014, 10:59 AM. -
Encode best practices, how many clusters?
Hello, SeqAnswers. I'm sure someone has a quick fix here. The Encode best practices guide suggests 30M paired end reads for simple D.E. and 100M+ paired... -
Filtering SNPs by coverage in HapMap format
I have data GBS derived from the UNEAK pipeline and I'd like to use the count.hmc file to remove SNPs from my HapMap.hmn file which fall below a given... -
Mutation Frequency vs. Depth of Coverage
Tumors are composed of malignant cells, stromal cells and immune cells. Accordingly, a tumor with a heterozygous mutation may only have 40% cancer cellularity... -
Filter mpileup for high depth of coverage without bcftools/vcfutils
Hi
I am working with Illumina paired end read data, several populations. I am creating an mpileup from several .bam files, each from a... -
GATK DepthofCoverage Error
Im trying to use GATK DepthofCoverage, but Im getting an error which I do not understand how to resolve.
My command is:
...Code:java -Xmx4g
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Problem with samtools depth?
I'm trying to plot the depth of coverage but when running samtools depth it seems to skip over bases which I presume have no alignments spanning those... -
quantitative expression study in twins
Hi all,
I am about to undertake a study investigating the gene expression differences between human twins using tissue from the pregnancy.... -
Counting reads (not coverage...)
Hi
Hopefully someone knows of some software or a script that will save me having to write one….
I want to put together some summary...
