Until now, specialised tools are required in order to access DNA...
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Use your standard DNA variant caller for SNP calling in Bisulfite-Seq data
Use your standard DNA variant caller for SNP calling in Bisulfite-Seq data
Until now, specialised tools are required in order to access DNA... -
Obtaining GVCF from bam files
Dear all,
My aim is to identify Runs of Homozygosity(ROH) in my samples. I kept getting 0 ROHs in both Plink and detectRUNs softwares... -
Bcftools Mpileup bias for alternative alleles?
I have called snps from a bam file using the below commands:
...Code:/usr/local/sw/bcftools-1.9/bcftools mpileup -f /mnt/NEOGENE2/share/ref/genomes/hsa/hs37d5.fa
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SNP calling from RRBS data
Hello,
I am interested in calling SNPs from reduced-representation bisulfite sequencing (RRBS) read data. The purpose of this analysis... -
SNP calling on samples sequenced with different technology
Hi,
is it possible to compare SNPs from alignments of different samples, whereas the samples weren't sequenced on the same illumina platform? ... -
Program to make consensus and call SNP?
Hello All,
I've got 2 distinct but related problems...well 3 problems if you count that I'm not a bioinformatician! I've just completed... -
SNPs at Interval Boundaries in GATK HaplotypeCaller
I'm using HaplotypeCaller with the -L option, where I explicitly state the interval. I am trying to break my task into pieces and assign it to different... -
SNP calling from RNAseq data
Hello NGS fellows,
I am a newbie here and would highly appreciate your advice about one particular experimental design.
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"bioinformatically pooling" replicates for SNP discovery from Pooled RNA-seq
Dear all,
What I have:
3 populations duplicate, 25M 100-PE reads each. That will be 6 libraries (using sample > 40 per lib) all... -
Where can I find sequencing data with known genotype?
Hello all,
I'm trying to find sets of public sequencing data with verified/known genotype in order to test my bioinformatics pipeline (for... -
mutect2 in a targeted region
Hi all,
I am using Mutect2 to call variants from exome seq samples (tumor/normal pair). I amusing the -L flag to call only in the targeted exome... -
Genotype calling within your sample set instead relative to reference genome
Hi there,
I'm developing a workflow to call variants from a dataset of ~600 samples sequenced through genotyping-by-sequencing (GBS) for...Last edited by Guillefriis; 11-04-2015, 07:11 AM. -
In-dels Illumina vs. PacBio
Hello,
I have a PacBio-generated closed complete bacteria genome. I am aligning Illumina reads of the same strain to it using breseq,... -
mpileup sample specific read count/quality info
Hello,
I am looking to use mpileup for base calling. Previously I ran samples together but could not find any sample specific read count/quality... -
SNP calling programs
Hello all,
I am a grad student at Texas Tech University and I have been tasked with reporting SNPs between 2 Listeria (bacteria)...
