14
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 ...
- 13.8k
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/...
- 281
6
votes
Variant calling without matched normal sample
If you just want to filter out calls present in dbSNP then use:
...
- 19.6k
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
- 19.6k
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.
- 19.6k
5
votes
Accepted
Does phasing improve imputation quality?
Yes. Phasing data leads to a better imputation accuracy. More specifically:
Improves allele matching: Correct phased data ensures that alleles are matched correctly between the reference panel and ...
- 827
4
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 ...
- 663
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 ...
- 19.6k
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)...
- 2,086
3
votes
Accepted
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 ...
- 1,021
3
votes
Accepted
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 ...
- 5,517
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 ...
- 2,086
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.
- 19.6k
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. ...
- 1,059
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 ...
- 5,517
3
votes
Accepted
Why might parabricks not be writing output to the output file I provided?
EDIT Summary
For future users who encounter the problem the solution is,
...
M__♦
- 11.9k
3
votes
Can we test the accuracy of Phred scores shown in FASTQ files
Yes, reported accuracy can be tested and compared with actual accuracy by mapping reads from a reference sample to a known-perfect reference sequence. It's usually done in aggregate, at a read level ...
- 13.8k
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 ...
- 2,324
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 ...
- 540
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 ...
- 13.8k
2
votes
Accepted
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 ...
- 1,304
2
votes
How to subset samples from a VCF file?
You can use the GATK's SelectVariants tool with the -sn flag.
E.g.
...
- 121
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 ...
- 465
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 ...
- 4,693
2
votes
Accepted
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:
...
- 19.6k
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 ...
- 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 ...
- 1,981
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 ...
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 ...
- 3,947
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