19 votes
Accepted

Converting a BAM file into VCF

It's not really possible to convert bam to vcf. bam is a mapping file, it does not contain ...
user avatar
  • 5,327
10 votes

How to detect a mutation and predict its consequence?

I'll follow up to the great answer from Kamil S Jaron: Regarding predicting what the variant ("mutation" is a very loaded term) will do, there are a variety of tools. Chief among these are annovar ...
user avatar
  • 19.2k
10 votes

What is indel calling and what is its purpose?

There are two types of INDELs: short indels and long indels. Some put the threshold at 50bp; others choose 1000bp. Short and long indels are called differently. <50bp short indels are called from ...
user avatar
  • 5,814
10 votes

How to subset samples from a VCF file?

Bcftools has sample/individual filtering as an option for most of the commands. You can subset individuals by using the -s or -S ...
user avatar
  • 11.9k
10 votes
Accepted

How to run same command on multiple files?

Another solution for repeating one command with different parameters is to use parallel. Create a tab-delimited file samples.txt...
user avatar
  • 1,332
9 votes
Accepted

What is indel calling and what is its purpose?

Insertions and deletions (indels) are one type among many different types of genetic variation, such as single nucleotide variants (SNVs), copy number variants (CNVs), and structural variants (SVs). I'...
user avatar
9 votes

How to detect a mutation and predict its consequence?

Part 1 : how to detect mutations The keywords you are searching for are "variant calling". Basically you have to map sequencing reads to a reference genome (or gene) and then estimate for each ...
user avatar
  • 5,327
9 votes
Accepted

Are variant calling files personally identifiable information?

TLDR: yes! be careful with someone's genomic data! There are two aspects to this question: can I find a match for a random VCF in a database of genomes (YES) or can I identify a subject who is not in ...
user avatar
8 votes
Accepted

How do I generate a variant list (i.e. VCF file) using Illumina reads from a human genome?

1. Adapter Trimming One of the first things I do after encountering a set of reads is to remove the adapter sequences from the start and end of reads. Most basecalling software includes some amount of ...
user avatar
  • 11.9k
8 votes
Accepted

How to quickly determine mutations in a read of a sam file?

For qualitative analysis, you're probably better off using something less granular like IGV or IGB. However, if you really want to look at a couple of reads: If you're willing to ignore sequencing ...
user avatar
8 votes
Accepted

How can I count the number of reads that support a variant in a bam file?

If you don't mind a bit of manual counting, then samtools mpileup -f reference.fa -r chr22:425236-425236 alignments.bam will produce output where you can count the ...
user avatar
  • 19.2k
8 votes
Accepted

Why Ti/Tv ratio?

I more like to use "ts/tv" for transition-to-transversion ratio. This abbreviation had been used in phylogenetics. When NGS came along, some important developers started to use "ti/tv", but I am still ...
user avatar
  • 5,814
8 votes

How to run same command on multiple files?

Something like this might do it: ...
user avatar
8 votes

Are variant calling files personally identifiable information?

Yes, definitely identifiable. The combination of ~80 unlinked common SNPs can be fairly unique in the entire human population, let alone the whole VCF file. EDIT: 30 in the original answer is an ...
user avatar
  • 5,814
7 votes
Accepted

variant calling on ChIP-seq style data: samtools mpileup with minimal filters

I used this in the past for ChIP-seq data and it generated SNVs: ...
user avatar
  • 2,099
7 votes

How to quickly determine mutations in a read of a sam file?

I wrote a program, ASCIIGenome, that I find handy in cases where you want to have a quick look at genomic data. It's a genome browser for the command line. To view only reads containing mismatches ...
user avatar
  • 649
6 votes
Accepted

How can I call structural variants (SVs) from pair-end short read resequencing data?

I think the best method or combination of methods will depend on aspects of the data that might vary from one dataset to another. E.g. the type, size, and frequency of structural variants, the number ...
user avatar
  • 952
6 votes
Accepted

Do variant calls change when you call from CRAM?

By default, a CRAM you create with samtools is lossless. It typically halves the input BAM in terms of file size. If you want to compress more, you can let samtools convert most read names to integers....
user avatar
  • 5,814
5 votes

variant calling on ChIP-seq style data: samtools mpileup with minimal filters

Another approach is htsbox. You can get a candidate list with: htsbox pileup -Cvcf ref.fa -q20 -Q20 -s5 file.bam > out.vcf Here, ...
user avatar
  • 5,814
5 votes

Is there a point in recalibration of scores for variant calling?

I personally don't think BQSR has a huge impact on variant calling, but you don't really need to guess. If you run GATK BQSR, it outputs a table and charts of exactly how much quality scores are ...
user avatar
  • 2,099
5 votes

Somatic tumor only variant calling?

I've been using the LoFreq* caller for exactly this. It is designed to find variants with very low frequency, so is well suited for this type of analysis. LoFreq* (i.e. LoFreq version 2) is a fast ...
user avatar
  • 8,161
5 votes
Accepted

Somatic tumor only variant calling?

There is a recent paper that attempts to do this: ISOWN: accurate somatic mutation identification in the absence of normal tissue controls. In this work, we describe the development, ...
user avatar
  • 727
5 votes

Selecting sites from VCF which have an alt AD > 10

using vcfilterjs and the following script: ...
user avatar
  • 1,473
5 votes
Accepted

Tool or script to parse annotated VCF files

(edit)you can filter the VCF annotations with snpsift, I've also written a VcfFilterSequenceOntology http://lindenb.github.io/jvarkit/VcfFilterSequenceOntology.html I've written vcf2table: http://...
user avatar
  • 1,473
5 votes
Accepted

Where can I get the population allele frequency vcf file?

On the GATK forum they've recommended the population stratified VCF file for this purpose.
user avatar
  • 19.2k
5 votes
Accepted

Tools to do VCF to MAF and MAF to VCF conversion?

Check this python script vcf2maf.py
user avatar
5 votes

Tools to do VCF to MAF and MAF to VCF conversion?

You can use annovar to annotate the vcf, then convert it to maf using the function annovarToMaf of maftools bioconductor package.
user avatar
  • 265
5 votes

Can a data file in VCF format be converted into FASTA?

You can try gatk function FastaAlternateReferenceMaker ...
user avatar
  • 3,551
5 votes

Converting a BAM file into VCF

You can use Freebayes, provided you have your BAM file and the reference genome. Example: freebayes -f genome.fa aln.bam > var.vcf I'd suggest you go through ...
user avatar
  • 2,656
5 votes

How to run same command on multiple files?

if you have a repeating workflow, I strongly recommend to have a look at workflow management systems like snakemake. I've also wrote a little tutorial on biostars about this topic, which might be ...
user avatar
  • 1,332

Only top scored, non community-wiki answers of a minimum length are eligible