# Tag Info

### 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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### 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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### 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 ...
Accepted

### 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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### 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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### 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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### 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 ...
• 8,111
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, ...
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### 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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### 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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### 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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### 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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### 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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### 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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### What is the name of this type of figure?

Such a figure is called ideogram, or chromosome ideogram.
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