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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 ...
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9 votes

Which tools can detect chimeric RNA (fusion genes) from WGS or RNA-Seq data?

Most of these use RNA-seq data, some use WGS data, and some use both. They are listed alphabetically. I will add to the list when I discover more. Barnacle: http://bmcgenomics.biomedcentral.com/...
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  • 281
6 votes

Variant calling without matched normal sample

If you just want to filter out calls present in dbSNP then use: ...
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  • 19.2k
5 votes
Accepted

Plot percentage of genome covered

The general steps are: Install deepTools Run plotCoverage on your BAM files Remove the left-most plot in photoshop/gimp/imagemagick
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  • 19.2k
5 votes
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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.
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  • 19.2k
4 votes
Accepted

What does this statement mean?

They created 10kb bins, which could be called "dividing the genome". These are just 10kb long contiguous stretches (so position 1-10000,then 10001-20000, etc.). This is, of course, a nonsensical way ...
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4 votes
Accepted

Removing common variants in the 1000 genomes database from .vcf

Use VEP, ANNOVAR or snpEff to annotate your VCF file (I'd recommend combining your VCFs into a single file if they're single sample VCFs or are all comprised of samples from the same experiment/cohort)...
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  • 1,367
3 votes
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Merging matched parts of two dataframes

If you have issue with memory and dealing with large object, maybe data.table is the way to go (https://github.com/Rdatatable/data.table/wiki): Let's take two ...
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  • 1,011
3 votes
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Extracting the number SNP in each range

There is like a thousand different ways how to achieve this. You could use a specialised software for this (like bedtools) or calculate it simply in R. R solution: You can make a function that ...
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  • 5,327
3 votes

Finding matched genes for each genomic range

You received an answer from Kamil for a similar question here: https://bioinformatics.stackexchange.com/a/8532/650 You can adapt the code they gave you to compare ...
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  • 1,367
3 votes

Which gene I should select from this qqplot

Given that TP53 is the most significant and is already known to have driver mutations in cancer it would seem to be the logical choice.
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  • 19.2k
3 votes
Accepted

Tumor purity/contamination/admixture estimation

I have previously estimated tumour purity with the EXPANDS an inferred tumour heterogeneity program which is designed to calculate the number of clonal subpopulations in matched tumour/normal samples. ...
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  • 1,029
3 votes

Obtaining Whole Genetic Sequence

"DNA data" comes in several forms dependent on the technology used to produce them. Companies like 23andMe are using SNP chips and those are available for an only rather a limited number of ...
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  • 5,327
2 votes

Tumor purity/contamination/admixture estimation

It's usually CNV callers that make use of Tumour/Normal WGS pairs to estimate purity. It can also be done with WES (exome) Tumour/Normal pairs. There are several tools out there, I have some ...
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  • 2,234
2 votes

How to compare groups using WGS data?

If you have gVCFs, the first thing you should try is joint variant calling. According to GATK, joint variant calling "empowers variant discovery by providing the ability to leverage population-wide ...
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2 votes

How to compare groups using WGS data?

I'm not familiar with the program, but apparently Hail is setting itself up as a swiss-army chainsaw project for doing downstream analysis on variant-called datasets. An overview of Hail can be found ...
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  • 11.8k
2 votes
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GATK documentation for required depth to reliably call heterozygous mutation in diploid organism?

UPDATE: As an update, Sarah Walker (co-author on the poster) responded to my question on the GATK forum. She clarified with the following statement: We believe ...
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  • 1,244
2 votes

How to subset samples from a VCF file?

In addition to the answer from @gringer there is a bcftools plugin called split that can do this, but gives you the added ...
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2 votes
Accepted

Plink 1.9 --merge-list changing order of fam file

Thanks Christopher Chang for the great answer via the plink2 google group! (See here) His answer was as follows: "Yes, plink 1.9 did change the default merged sample order. However, you can request ...
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  • 445
2 votes

Which gene I should select from this qqplot

You can't know which is the driver and which is the carrier. At most you can say that a specific gene deviate more of the expected underlying hypothesis. See also other resources online. You also ...
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  • 4,622
2 votes
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Generate table for total number of SV events per sample

So you have data in "long format" and want to convert it to "wide format". You can use spread() from tidyr for that: ...
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  • 19.2k
2 votes

Common QC parameters and threshold in human WGS pipeline

I would suggest you look at the website for the excellent MultiQC tool (https://multiqc.info/). We use it in a clinical setting to collate all the QC statistics from our pipelines into a single ...
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  • 181
2 votes
Accepted

Looping over several files in bash

If we save the script pasted in the main post as a sh file and we have some .vcf files in a folder, by this line we can iterate over vcf files to extract what mentioned in the script returning .txt ...
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  • 1,697
2 votes

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

What is the difference of ReadCount in INFO column and DP in FORMAT column? I'm not super familiar with Strelka but I believe it follows the VCF spec, so DP in the FORMAT column should give the depth ...
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2 votes
Accepted

Making a boxplot or violinplot for several dataframe with different number of samples

To help us help you, please make your data available with dput() next time. To achieve your goal with ggplot2, you would need ...
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  • 3,477
2 votes

Joining columns to a sorted file

Rearrange your text file into a sorted BED file: ...
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2 votes

How to find all WGS assemblies accessions of a species

There seem to be WGS assemblies that can't be found in NCBI Assembly database, e.g.: https://www.ncbi.nlm.nih.gov/nuccore/1779902990. I guess that such assemblies also cannot be found in The ...
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2 votes
Accepted

Obtaining Whole Genetic Sequence

Are you looking too far ahead into the future? No. This is certainly possible now. The gold standard being Illumina or BGI short read WGS. Long read sequencing can capture some extra data but is very ...
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2 votes

Best practice for running GATK VQSR on X chromosome

You are correct that differences in ploidy between autosomes (always ploidy=2) and X chromosome mean that the same VQSR model cannot be applied to both cases equally. However, this is the case only ...
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