I have a FASTQ file whose quality is summarised in the following graphs. ![enter image description here][1] ![enter image description here][2] I understand that if …

I was looking at the VCF format 4.3 [here - page 7](https://samtools.github.io/hts-specs/VCFv4.3.pdf) and 4.2 [page 4](https://samtools.github.io/hts-specs/VCFv4.2.pdf). More or less they are similar, stating **8 mandatory …

I'm trying to download reference annotation data --specifically bed files for exons/introns in the mm10 genome, and I saw [this question here][1] saying that you …

Dear, I recently apply my attentions on analysis of structure variants (SV) with called vcf file. I have read the The VCF specification V 4.2 …

Job Location: UCSC Santa Cruz, CA 95064 http://genome.ucsc.edu Job Description: The incumbent will be responsible for supporting and extending major subsystems of the UCSC Genome …

Job Location: UCSC Santa Cruz, CA 95064 http://genome.ucsc.edu Job Description: The incumbent will be responsible for supporting and extending major subsystems of the UCSC Genome …

<p>The <a href="http://samtools.github.io/hts-specs/SAMv1.pdf#page=3">SAM/BAM specification</a> says that one can mention the genome assembly of a reference sequence, the species, etc. For this, one only has to …

Mostly a curiosity question but: 1. Is the cigar '=' op kept for backwards compatibility or some specific use-case? 2. Is there functionality within samtools …

Hi all, I'm struggling with finding explanations to the SAM flags presented on my sam file. to clarify, I am familiar with [the picard tool][1] …

<p>Hi,</p> <p>I downloaded a list of <code>refseq genes</code> from the <code>table browser</code> - <code>UCSC</code> in <code>bed</code> format. From the bed format description given by UCSC, …