Hi,
Can anyone please help me understand why i get ID the same names in VCF file (mine is SV from svaba) with name:1 name:2, .Isn't that the same...
14 results in 0.0021 seconds.
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Genome Assembly
I have Illumina sequenced paired-end reads of an arthropod genome. I already mapped my reads to the reference genome and generated a BAM file and a variant... -
Convert vcf to bed based on PS field
Hello,
I want to convert the VCF file with phase information into a phase block bed format.
So if this is the file:
#CHROM... -
Accessing Genomic data in a large vcf.gz file
Hello all, I am very new to bioinformatics; I'm a high school intern. I have a .vcf.gz file that is 332 GB. It contains the whole genomes of around 800... -
No mutations in BAM (IGV) but a mutation in final VCF?
I use GATK 4.0 for the variant calling pipeline. my steps involve MarkDuplicates, BaseRecalibration, ApplyBaseRecalibration and HaplotypeCaller. When... -
A problem of using Samtools to make VCF file
Hi!
I used the samtools commands and 1000 genome data(phase 3, low-coverage sequenced data) to generate the VCF file for both snp and... -
VCF file missing GT field - How to fix?
Hi,
I am using GATK DiagnoseTargets to get some stats about the coverage of my reads compared to an exome interval list.
For... -
COSMIC vcf file contains "N" & "." characters in ALT column
Hi,
I am using COSMIC hg19 vcf file to make hotspot bed file but in ALT column of COSMIC vcf contains "N" & "."... -
Haplotype frequencies
I am interested in looking at some very short regions (~200 bp) in the human genome which contain ~15 SNPs. So, taking for instance Phase 3 phased haplotype... -
Has anyone used kSNP?
Hi all,
I'm using kSNP to call snps in my data and generate a vcf file of the outcomes.
I have a reference genome which i have used prokka... -
Understanding the values in a VCF
Hi all,
In my generated VCF file (from samtools mpileup) some of my info fields are these:
My question is... -
Samtools and bcftools: Why aren't some of the calls "missing data".
I'm using samtools mpileup and bcftools view to find variants. I'm perplexed why none of the alleles for any of the samples are shown as "missing... -
vcf-compare output
I am looking at some VCF files; I like the output from vcf-compare, eg:
#SN Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this... -
mutation id in the vcf file
I have the .vcf which is generated by GATK on the sample. I need to get the transcript and accession ID of those in the bed format, that is needed for...
