13 votes

using python to write bioinformatics pipelines tutorial

Taking a different tack from other answers, there's lots of tools for pipelines in Python. Note: there was a time when people would use "pipeline" to refer to a shell script. I'm talking about ...
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  • 758
13 votes
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The state, limitations and comparisons of large variant stores

An epic question. Unfortunately, the short answer is: no, there are no widely used solutions. For several thousand samples, BCF2, the binary representation of VCF, should work well. I don't see the ...
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  • 5,735
8 votes

ethnicity check either from bam or vcf files

The main difficulty here is the use of GRCh38. Unfortunately, despite the fact that it's more than four years old, the major ethnicity-labeled public datasets (1000 Genomes, gnomAD when allele ...
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6 votes
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How to filter out cross alignments from a BED file?

According to the SAM specification, the 3rd field of a SAM line (RNAME) is: RNAME: Reference sequence NAME of the alignment. If @SQ header lines are present, ...
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  • 8,111
6 votes
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What is the name of this type of figure?

This kind of visualization showing the banding patterns of chromosomes are called "chromosome ideograms". You can use for example IdeoViz in R to generate them.
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  • 768
5 votes

Using BLAT command line tool to blat split sequences

The FAQ offers an answer: I'm setting up my own Blat server and would like to use the same parameter values that the UCSC web-based Blat server uses. We almost always expect there to be some ...
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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 ...
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  • 8,111
5 votes
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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, ...
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  • 727
5 votes

Range overlap python error with genomic regions

You're reinventing bedtools intersect (or bedops), for which there's already a convenient python module: ...
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  • 19.2k
5 votes

using python to write bioinformatics pipelines tutorial

BioPython has some good tools for processing reads and alignments. http://biopython.org/DIST/docs/tutorial/Tutorial.html There is a python library wrapping samtools so many of the samtools calls can ...
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  • 2,556
5 votes

Selecting 65000 SNPs where AF is close to 0.5 in all or most populations

Just use bcftools view for filtering: $ bcftools view -i 'AF>0.3 && AF<0.7' input.vcf.gz > output.vcf To truncate this list to 65,000 SNPs count ...
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  • 1,332
5 votes

What do the FASTQ file names mean here?

What is "S13"? S# is most likely the sample number. If so, you do not want to combine these. What is "L002_l1"? L00# is the lane number (of the 8 Illumina flow cell lanes). 'I1_' (not 'L') are ...
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  • 2,574
4 votes

using python to write bioinformatics pipelines tutorial

If you're just doing alignment and conversion to a sorted BAM file, there's no need to run it through python. A simple pipe on the unix command line works just as well (and probably runs faster): <...
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4 votes
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Installing Sibelia for Ragout on Mac OSX

There is a link to compiled binaries for OSX on the project homepage
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  • 1,806
4 votes
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What does "motif 2 bp or longer" mean?

What's your reference for the definition of STRs? I think it is still ambiguous among the community. Wikipedia states motifs of >=2 bp. However other references include homopolymers as well: Source 1, ...
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4 votes
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using python to write bioinformatics pipelines tutorial

I agree that using a specialized tool is probably a good idea. Nevertheless if you want to stick with Python, I suggest using plumbum instead of ...
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4 votes
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Generating DNA sequences with constraints

You can use a $l$-order Markov chain. Here is the procedure: Count $l$-mers in your genome. For small genomes, you can do that in Python. For large genomes, you may need jellyfish or KMC3. Draw a $l$-...
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  • 5,735
4 votes

what is the most complete vcf file of population allele frequencies that can be built/downloaded from public datasets?

The best set I'm aware of can be downloaded from https://gnomad.broadinstitute.org .
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4 votes

What are the coordinates of the extended major histocompatibility complex (xMHC) in GRCh38?

Here is one definition of the classical MHC region: https://www.ncbi.nlm.nih.gov/grc/human/regions/MHC?asm=GRCh38.p13 which defines it as the 5mb region chr6:28510120-33480577 in GRCh38 coordinates. ...
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3 votes
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Genomic coordinates of predicted binding pocket

It turns out there is a tool that does this beautifully. I used the proteinToGenome function from the ensembldb package. The code looks like this: ...
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  • 841
3 votes

Path to career in bioinformatics?

The Bioinformatics Stronghold at Rosalind is an excellent resource for building your understanding of many concepts and algorithms you'll see frequently in bioinformatics and genomics. I'd also say ...
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3 votes
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Command not found error on HISAT2

tldr: Remove the $ from the command. I imagine you're literally typing $hisat2, where you mean to instead type ...
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  • 19.2k
3 votes

Range overlap python error with genomic regions

Regarding your python code If you want the experimental ranges that are entirely contained in one of the reference ranges, you need to have the coordinates in the following order: ...
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  • 2,960
3 votes

How to adapt the fgseaL function to perform rapidGSEA computation of gene ranks across 9 different phenotype labels?

I finally found another answer to my question. Please read this great article in May 12 2017 BioMed Central (BMC) Bioinformatics article titled Ranking metrics in gene set enrichment analysis: do they ...
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  • 191
3 votes

Genomics: Downloading genomic data from the NCBI Genbank database

For downloading data from commandline use the E-utilities of NCBI.
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  • 273
3 votes

Selecting 65000 SNPs where AF is close to 0.5 in all or most populations

Using bcftools is the right way, but you could also greatly simplify the command you're using. You can do the same thing with a single ...
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  • 8,111
3 votes

Does UCSC definition for telomere making sense?

It seems so, yes. UCSC uses a 10Kb definition and representation for telomeres in human. In the table you shared this is consistent across all chromosomes, not only chr21. This 10kb representation ...
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  • 353
3 votes

What is the name of this type of figure?

Such a figure is called ideogram, or chromosome ideogram.
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  • 3,541
3 votes

Are there genomics databases for neurological and psychiatric disorders?

Try with PsyGeNet: PsyGeNET (Psychiatric disorders Gene association NETwork) is a resource for the exploratory analysis of psychiatric diseases and their associated genes It is based on literature ...
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  • 1,012
3 votes
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>My counter is counting genotypic combination occurences more than once, how do I ensure it counts one combination and doesnt count it again?

Alright, so there are a number of problematic patterns in your code - as far as I understand what you are trying to do. Next time, try to post a reproducible example that people can use and more ...
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