Questions tagged [snv]

The tag has no usage guidance.

Filter by
Sorted by
Tagged with
13 votes
3 answers
369 views

Given a VCF of a human genome, how do I assess the quality against known SNVs?

I'm looking for tools to check the quality of a VCF I have of a human genome. I would like to check the VCF against publicly known variants across other human genomes, e.g. how many SNPs are already ...
ShanZhengYang's user avatar
9 votes
1 answer
159 views

Expected allele frequency distribution of SNVs in real NGS data

I have a huge amount of ~20x human WGS samples, aligned, and all SNVs that were called with GATK under standard germline parameters set. What I need to do is to model SNVs Allele Frequency (AF) for ...
German Demidov's user avatar
2 votes
1 answer
220 views

somatic SNV tool for ONT samples

I'm looking for a tool to call somatic single nucleotide variations on reads from an Oxford Nanopore Technologies (ONT) run. I have both tumor and normal samples and have already aligned them to a ...
Walter Gallego Gómez's user avatar
2 votes
1 answer
113 views

Is it common to get different number of SNVs+Indels across samples from vcf files generated using GATK and DRAGEN (counts are higher for GATK)?

We have 2 vcf (Whole Exome Sequencing (WES) data; germline samples) files (e.g., vcf_1 and vcf_2). vcf_1 was generated (Ref. genome: hg38) using the GATK pipeline for 250 children and their parents ...
App.vsh.io's user avatar
2 votes
0 answers
49 views

state-of-the-art methods to obtain SNVs from circulating tumor DNA?

What is the state-of-the-art to obtain SNVs from circulating tumor DNA after Illumina sequencing? This is, finding a list of nucleotide locations that show tumour SNVs filtered out of any germline ...
719016's user avatar
  • 2,324
1 vote
2 answers
74 views

Merging matched parts of two dataframes

I have a big data frame like this ...
Zizogolu's user avatar
  • 2,148
1 vote
1 answer
328 views

Help with the definitions of fields in a VCF output by Strelka

In Strelka vcf in INFO column we have these ...
Zizogolu's user avatar
  • 2,148
1 vote
1 answer
137 views

Tumor sample and heterozygous SNVs: what is the genotype of the normal cells?

In the following picture, you can see that in normal cells (yellow) we have two copies of each gene, while in tumor cells (violet), we just have one copy due to a clonal mono-allelic deletion. I do ...
wrong_path's user avatar
0 votes
1 answer
1k views

What are values of FILTER column of vcf files produced by Mutect2

I have called SNVs with Mutect2, now in filter column of a file called filtered vcf I have a lot of things like ...
Zizogolu's user avatar
  • 2,148
0 votes
2 answers
508 views

Parsing .vcf file for this information

I have a .vcf file https://www.dropbox.com/s/8v73nppwg3a1tnd/LP2000109-DNA_A01_vs_LP2000103-DNA_A01.SVannotated.txt?dl=0 with this header ...
Zizogolu's user avatar
  • 2,148