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5,171 results • Page 1 of 104

Hello, I want to estimate allele frequency at different read depth (10X, 20X, 30X, and so on). I have variants call output in vcf format. I also estimated read...depths for all SNPs. I am thinking to subsets the vcf at different depth for e.g. 10X, 20X etc. I am not sure if this is a correct way...to proceed. Is there any better way to estimate allele frequency at different depths? Any suggestio…

allele depth frequency vcf read

updated 2.9 years ago • rthapa

The VCF header says AD: Allelic depths for the ref and alt alleles in the order listed I understand what "read depth" and "allele" are, but I do not quite...understand what "allelic depth" means. I've read both VCF4.0 specification and VCF development history, but none of them had the answer

read allele genome

updated 7.4 years ago • Chronos

I have vcf file where the allele depth and depth do not match. Why is this? Here is the offending line.... > chrX 155252833 . G . 81 . DP=12;AD=10;MQSB=0.183296;MQ0F...0.333333;AN=2;DP4=7,3,0,0;MQ=6 GT 0/0 DP is the depth, right? In this example DP is 12. So how come AD is 10

vcf

updated 6.1 years ago • b10hazard

I am attempting to get the Allele Depth (AD) from my vcf file. I got this file from bcftools file using the function: bcftools view -c -g scaffold_filt_PV003_q10_variant.bcf...called format does not appear AD, only appear GT:PL:GQ I do not another alternative way to see Allele Depth. Thanks in advance

SNP bcftools vcf

updated 5.0 years ago • apl00028

I'm looking for VCFs that has sample-level allelic depth information. Something similar to GATK Haplotype Caller. I would like to know the number of reads supporting...this information (phase 3 low coverage samples is preferred) Or did 1000 Genomes not report the allelic depth for the variants? I tried looking around and the only think I could find was a VCF with DP annotation (depth of covera…

AD GATK GATK HC 1000 Genomes

updated 8.0 years ago • QVINTVS_FABIVS_MAXIMVS

Hi, I am trying to filter my GATK 4.0.3 - HaplotypeCaller generated multi-sample VCF for allele depth (AD) annotation at sample genotype-level (so available in "FORMAT" fields of each sample). I think prior to GATK 4, this...annotation was available as "Allele Balance" (AB) ratios (generated by AlleleBalanceBySample), but it is not available anymore in GATK 4. So I tried to filter...format, so …

gatk filtering sequencing allele depth

updated 5.9 years ago • maegsul

Hi All, For the below vcf record, first sample is G/G (1/1-Heterozygous alternate) with allele depth of 101 reads. Whereas for the second sample is also G/G(1/1) with allele depth of 1 read. Overall depth is 102. If I filter...has only one 1 supporting read. 1) For multisample VCF, should I filter the variants based on allele depth (AD) or Overall depth (DP)? 2) What is VQSRTrancheBOTH99.00to…

VCFs SNPs Variants Depth DNASeq

updated 7.8 years ago • bioinforesearchquestions

in the VCF file is that despite having only 2 genotypes separated with "/" or "|", the number of allelic depths (ADs) is larger than the number of alleles (i.e., in the example below 3 ADs for 2 alleles or 4 ADs for 1 allele in the...1933943_TTAAGGTAG_T:139,139,139,139,139,139,13,13,13,0:1933943 I thought that in this case only the depths for alleles 1 and 2 (or for the allele 3 in the second e…

VCF GATK Genotyping Variant-calling

updated 11 months ago • Alexandros

CNV identified by depth but can not be identified by snp allele frequency. Depth support that there is one allele of Amplification in chromosome

genome CNV sequencing ASCAT

updated 2.3 years ago • wangjiaqian

if anyone knows how to filter heterozygous genotype calls from a vcf file where, for either allele, there is only one read supporting the call. So the allelic depth would be n,1 or 1,n. n meaning the depth could be anything

vcf SNP next-gen alignment

updated 10 months ago • molly.dunn

we already have a set of SNPs called in a matched normal bam file, is there a way to extract the allelic depths in a tumour bam in the form of VCF without running variant calling in both bams? I understand that this is probably

bam VCF

updated 2.3 years ago • mikothebichon

We checked several alleles (locus) in both bam and vcf file. Almost all of them show a little bit high depth in bam file and a bit lower depth (AD) in vcf

allele depth bam vcf variant

updated 6.0 years ago • CY

question, but I am currently trying to filter a VCF by what variants a specific sample has a variant allele depth above 3 for. I've been able to use bcftools to filter variants by if any samples have a variant allele depth above

bcftools VCF

updated 2.8 years ago • john_campbell1

output. As was suggested, I should filter the variants based on the bam readcounts (or read depth or allelic depth?). I'm confused of the definition and the discrimination among these three terms. Is the bam readcounts

bam vcf sequencing genotype

updated 3.1 years ago • lincaijin1994

Hi, I had a question about Allelic depth (AD) of BCFtools. It has this format e.g. AD=262,18,0 - What number shows the depth of the REF and what is the ALT? and what

Allelic Samtools BCFtools Depth AD

updated 2.6 years ago • christiangriffioen

Hi, I'm new to the subject. I got a sam file and fasta file, I need to get all the allele `ref = G` `alter = T` with a specific depth. As I understand it I need to use samtools, but I never worked with it..can anyone get me

sam samtools

updated 13 months ago • sahar850

Is there a quick way to get allele read depth for all possible alleles say from bam or mpileup? 10 101023 . A G,T 220 . DP=35;VDB=0.0407;AF1=1;AC1=2;DP4=0,0,14,11;MQ

allele counts

updated 10.6 years ago • Rm

definition to consider hom based on AD. A lot of variants are defined hom if they have very few REF alleles, but in some cases I saw that, as example, a `92,342 (ref, alt)` is considered `1/1 (hom)`, and also some `56,227`or `7,31` etc I imagine it...depends on some kind of ratio amongst total read depth and altered depth, but I was wonder which threshold is normally used. Thanks in advance for…

hom het AD count variant

updated 5.0 years ago • cocchi.e89

Hello I am dealing with the whole exome data, and want to filter out the variants whose depth of coverage for alt divided to ref allele (alt/ref) is less than or equal to 30%. This is what the .tsv file looks like: chr1 45797228...Column 14* ("**37,31**") is the column of my interest. 37: depth of coverage for ref allele, 31: depth of coverage for alt allele Would you please…

Data Coverage WES Filtering

updated 14 months ago • Fatemeh Nabizadeh

GT:GQ:DP:PL:AD (order of terms in file) where GT = genotype, GQ = genotype quality, DP = read depth, PL = phred-scaled genotype likelihoods, AD = allelic depth For example, suppose that my file has the following entry (with

vcf depth-of-coverage

updated 10.9 years ago • C00101

PL : List of Phred-scaled genotype likelihoods GQ : Genotype Quality Is it possible to add the Allelic Depth information (AD) in the VCF file ? Is there an option for this ? GT : AD : PL : GQ Thanks

samtools allele vcf

updated 9.6 years ago • Scubnoucca

I also have more than 1000 snps in snp table as shown below. I need to get the number of reads (allelic depth) for reference allele and alternate allele from all the bam files. Is there any program to get that directly from

bam sequencing genotype

updated 20 months ago • MAPK

a few other callers) to look for somatic variants, we are getting multiple cases where several alt alleles are identified at the same position (on same single line in VCF). When we try extracting info from VCF (through Gemini...database), we can't get any additional info for those variants with multiple alt alleles at same position. In the VCF, I can't see any allele depth. Why are we getting a…

next-gen alignment genome software error

updated 6.6 years ago • charles.meuniercm

Hello everyone, I was wondering if you could help me with an analysis I've been doing on some alleles. My project consists on determining the presence/absence of 5 different alleles in malaria, however I've found it hard...to find the threshold of which allele is actually there and what is noise. For my analysis, I used a set of .fastq files (20 of them) and input them in a SRST2 (similar...to M…

NGS Deep sequencing Post genomics next-gen

updated 5.1 years ago • dann.dignus.discere

a vcf file with these values GT:VR:RR:DP:GQ in the format field. I would like to add the Variant Allele frequency tag (Frequency of alternate allele). I know that I can calculate it manually from the read depth information...FREQ=(DP-RR)100/DP where DP: read depth and RR: reference read depth. Do you know any way to do it with commands (bcftools,vcftools or awk)? Thanks

next-gen

updated 4.2 years ago • nikimourtzi23

Pindel (0.2.5b9, 20160729) for somatic DNA to detect internal tandem duplications (ITDs) at variant allele frequencies (VAFs) in the range of 5% and greater. The vcf files produced by pindel2vcf always report 0 as the allele depth...AD) for the reference allele. Supposedly Pindel's VCFs also have a "reference depth" metric (RD) but this is not actually reported. I cannot find anything...in the r…

Pindel

updated 4.2 years ago • myourshaw

use the bam and just the bed file and target I have to extract all the information like total read depth and allele frequency, any help is greatly appreciated. I am a newbie to this

bed bam mpileup allele-frequency

updated 16 months ago • bobrowdy123

Hello, Can someone explain me this step that scientist have done. > Then, only bi-allelic SNPs (variant quality score > 200, cumulative depth > 200, individual allele depth R 3) were taken into analysis, and...those were further subsetted to cases where an alternative allele was absent in time point 1, to simplify calculations of mutation accumulation rate. This is from th…

next-gen sequencing gene

updated 4.2 years ago • vishalchanda364

problem in my vcf file produced by GATK: a large proportion of heterozygous sites has a bias in allele depth values (AD). For example, AD is 43,7 which means that the 43 reads support one allele while 7 support another. In order...the heterozygous calls (0/1) for no-calls (./.) in case of significant AD bias, let's say when minor allele to major allele ratio is greater than 0.3. However, I wonder…

vcf GATK heterozygous SNPs Allele depth AD

updated 3.1 years ago • rimgubaev

I have a vcf file with SNPs called using the Torrent Variant Caller and I want to calculate their Variant Allele Frequencies. The issue is that there is both a DP (depth) and a FPD (flow depth) fields as well as an AO (Alternate Allele Observations) and a FAO (Flow Alternate Allele Observations) fields and the two often disagree by a lot. Which pair should I trust? DP & AO or FDP &a…

snp sequencing vaf Ion-Torrent

updated 20 months ago • stamakro

read like and individual) but it doesn't seem like that will work here. Maybe I should just plot allele frequencies? Is that calculated by doing AF = AD (allele depth) / DP (read depth) from the VCFs? Or what is the best way to find

variant-analysis

updated 6 months ago • kristina.mahan

140,2570,0,0;QS=1,0;MQ0F=0 PL:ADF:ADR 0,27,86:0,0:9,0 See the above line for example. Here the depth is DP=15, however allelic count on forward strand and reverse stand is 0, 0 and 9, 0, and sum up to 9 < 15. Why this happens? Thanks

samtools vcf mpileup

updated 7.3 years ago • mt1022

just stay as whatever original orientation they have (case 1 below)? I am trying to find the mutant alleles in BAM, so wondering should I check both orientations. ``` A to G SNV: is it ---------------A------------- ---------------G--> <-------C---------- or? ---------------A------------- ---------------G--> <-------G---------- ``` 2. When we compute t…

SNV DNA VAF sequencing mutation

updated 22 months ago • robinycfang

Hopefully there are some Strelka users out there who can help with this one. I'm looking for allelic counts of the ref and non-ref allele of the indels. I see these flags in the VCF header, do these give me the information...I need? ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth for tier1"> ##FORMAT=<ID=DP2,Number=1,Type=Integer,Description="Read depth for ti…

somatic indel

updated 10.0 years ago • Richard

Hello, With 30X depth NGS sequencing, what is the chance at one position that an allele is not sequenced at all with 30 reads ? Should we do 2^30

sequencing

updated 2.5 years ago • vpsev3

I got a VCF which I need to calculate variant allele frequency for each variant at each position. My understanding is that variant allele frequency is AD / DP There are multiple...VCFv4.1 ##INFO= <id=dp,number=1,type=integer,description="approximate (reads="" are="" bad="" depth="" filtered)"="" mates="" mq="255" or="" read="" with=""> ##INFO=<id=ad,number=1,type=integer,description=…

vcf allele-frequency

updated 12 months ago • jason

deletion, amplification, copy neutral LOH, ... The simulator has two parts: simulation of the read depth (this part is already implemented) and simulation of beta allele fraction (BAF) (under development). To develop the second...events. For instance, if there is no aberration, I expect p to be 0.5 (0.5 for seeing the reference allele and 0.5 for seeing the alternative (b) allele) etc. The outp…

statistics allele simualtion snp baf

updated 2.3 years ago • Dataman

Hello Everyone, I have a VCF file that has no DP info only AD (allelic depth). Does anyone know of a way that I can get per sample mean read depth using only the AD filter? I could write a custom

vcf coverage depth

updated 7.9 years ago • Rubal

I have a VCF file that has no DP info only AD (allelic depth). Does anyone know of a way that I can get per sample mean read depth using only the AD filter? I want a custom script

VCF

updated 18 months ago • tasnimul35-241

Hi, I have a multisample vcf that I would like to filter based on read depth. More precisely, I would like to modify the vcf so that a snp that is detected where the read depth is more than the average...read depth at the sample will change to the reference allele. I know how to filter snps where read depth is higher than a certain value

vcf filter variant call read depth

updated 6.4 years ago • agathejouet

per sample and sequenced with novaseq. I want to know the optimum number of individuals and optimum depth for each sample. I am planning to subset different coverage like 10X, 20X etc from bam file to find the appropriate read...depths comparing the allele frequency and heterozygosity across different depths. Do you have a any suggestion on how to

depths number of genotyping read

updated 2.9 years ago • rthapa

all, the very basic question: I have genotyped SNVs and for each 0/1 variant I want to extract the depth of coverage and the read counts of both alleles. How to do it "in a universal manner", in other words - for any genotyped vcf...mater how it is formatted? In our VCF files there is AO field in FORMAT column with contains minor allele count - that's fine, but I can not find this field in the o…

vcf

updated 4.5 years ago • German.M.Demidov

Hello! I am having a problem while estimating the depth of coverage in my data using `samtools depth` and `samtools mpileup`. I got paired reads and performed sorting and indexing...of the BAM files. However, when I use `samtools depth` and `samtools mpileup` to estimate the depth of coverage at specific coordinates, I get significant differences in the...results. For example, the depth of …

samtools mpileup depth

updated 11 weeks ago • Ирина

identify SNPs within 3 separate individuals and have generated a VCF file. I am able to extract the depth for each individual but am struggling to get the allele frequency at each SNP for each individual. The VCF contains an...overall alternative allele frequency but I would like this broken down per individual. If anybody knows if this is possible and how to do it I'd be

snp vcf samtools

updated 12.0 years ago • Jitendra

Hi, Generally, in cancer variation studies, the variant allele fraction (VAF) is calculated using this formula: alt reads/total reads at the loci. In a VCF file, the FORMAT/AD tag has two...values, for ex., 43,45 where the numbers represent allelic depths for the ref and alt alleles for a sample in the order listed. The FORMAT field also has the DP tag which is the total...depth. The differe…

VCF snp

updated 3.2 years ago • prasundutta87

is there a parameter in variant calling where we can specify to not call variants if the reference allele frequency is say >0.8 than the alternate allele frequency? I ask this because I am getting few SNPs which are called...according to ClinVar but it does not get validated using Sanger sequencing. So I checked its allele frequency ratio and it shows that reference and alternate allele f…

SNP vcf

updated 5.9 years ago • bioinfo89

I am using samtools depth to get read depth at each position from the bam file which I have after doing alignment. I used the command: samtools depth...a -H input.bam -o output_duplicates Since my bam file comprise more than one sample, how samtools depth will calculate the read depth? The output file I have consist of three columns with the first column chromosome, second...position and third …

sequencing RNA-Seq

updated 3.2 years ago • bandanaschapagain

SNPs using GATK, and have observed that in many 1/1 SNP sites (homozygeous alternate) the whole read depth (stated in DP) are supporting the the alternate allele (as seen in the AD field), while the reference allele is supported...by 0 reads. So how GATK called this ref allele if there is no reads supporting it. Example: ![Example][1] [1]: /media/images/cb623a4d-23f3-4b28-b415-00260918

SNP GATK

updated 11 months ago • mohsamir2016

a few relevant lines from the actual file: ##INFO= <id=ac,number=a,type=integer,description="allele allele,="" alt="" as="" count="" each="" for="" genotypes,="" in="" listed"="" order="" same="" the=""> ##INFO=<id=af,number=a,type=float,description="allele allele...listed"="" order="" same="" the=""> ##INFO=<id=an,number=1,type=integer,description="total alleles=""…

frequency allele VCF

updated 15 months ago • Emoji

down to 0.1%. An easy answer to our goal could be to do whole genome sequencing with very high depths in all IDs. But I am more interested in the idea of applying low depth (appr 4X) whole genome sequencing combined with an...array based genotyping assay. Applying low depths sequencing, results in high uncertainty in the called genotypes and it will be almost impossible to estimate allele...p…

next-gen sequencing array imputation statistics snp

updated 13.0 years ago • Thomas

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