Hi all,
I'm using NGS data to observe how a community of congenic bacteria evolve over time. Basically, I'm starting by inputting several...
33 results in 0.0023 seconds.
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Detecting Known, Low Frequency SNPs in evolving bacterial communities
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call indel and SNP by varscan
Hi all,
I met problem when I work on a 7M bacterium genome. I mapped 140x of paired-end reads (151x2) from illumina to a Pacbio reference... -
how is ABQ - Average quality of variant-supporting bases calculated in the Varscan?
How is ABQ - Average quality of variant-supporting bases calculated using Varscan? And also Can anyone tell me what is the scale( phred ??) of the ABQ... -
Hardware requirements for various tools
Hi All
New to sequencing.
I am planning on running BWA, GATK and possibly VarScan.
Does anyone know what are the hardware... -
bam-readcount warning
hi everybody,
i am using bam-readcount to filter out false positives from snp calling.
i am getting (sometimes almost 5million)... -
problems with varscan2.3.7
hi,
i am using varscan in the following command for germline/somatic calls:
samtools mpileup -q 20 -Q 20 -f hg19.fa -B file_norm... -
VarScan2. Strange behaviour of somatic-p-value
Hi community of SEQanswers,
I'm running varscan2 for somatic mutation calling following the commands of its documentation: mpileup + varscan...Last edited by slois; 04-03-2014, 08:01 AM. -
VarScan- invalid format for pileup
Hello,
I've used the following command to filter my BAM file, run samtools pileup and varscan:
samtools view -b -q 10 myBam.bam... -
VarScan somatic indel caller working incorrectly?
Hi
I am seeing a seemingly incorrect somatic indel call using VarScan somatic.
The VarScan output line is
chr2 178883096 T +TAAC... -
VarScan: somatic mutations in heterozygous sites?
Does VarScan2 find somatic mutations that arose in loci where norm was heterozygous? As far as I can tell, it classifies somatic changes as "Somatic"... -
Filtering steps for VarScan2 somatic and germline calls
What is the proper filtering pipeline for somatic mutation detection using VarScan2, with tumor/normal paired samples?
My understanding of the... -
vcf files merging
Hi all,
I was wondering which is the easiest way to merge multiple vcf files (outputs of Varscan). I have some vcf files listing all the... -
unalble to clone repository for bam-readcount from github
Hi all,
I am using varscan somatic and i need to use the fpfilter for which I need read count from bam-readcount program.
When...Last edited by ashwinipatil; 03-14-2013, 11:35 PM. -
VarScan early halt
Hi,
I'm new to VarScan. I was trying to call copynumber from my exome sequencing data.
My script is
samtools mpileup... -
Samtools mpileup - start and end segments
Hi,
I'm having a problem calling a variant with NGS which has been confirmed via Sanger sequencing.
I'm using samtools mpileup...
