Copy-number variations (CNVs)—a form of structural variation—are alterations of the DNA of a genome that results in the cell having an abnormal number of copies of one or more sections of the DNA. CNVs correspond to relatively large regions of the genome that have been deleted (fewer than the normal number) or duplicated (more than the normal number) on certain chromosomes. For example, the chromosome that normally has sections in order as A-B-C-D might instead have sections A-B-C-C-D (a duplication of “C”) or A-B-D (a deletion of “C”). Source:

Synonymous and Non-Synonymous SNPs

To be a synonymous or a non-synonymous SNP, the SNP must fall inside a protein-coding region of the DNA (otherwise it is a noncoding SNP). A synonymous SNP is a coding SNP that does not change the protein sequence. A non-synonymous SNPT is one that changes the protein sequence. So what you have to check is if the SNP changes a codon to a different codon for the same amino acid, in which case it is a synonymous SNP, or if it changes the codon to one that codes for a different amino acid, in which case it is a non-synonymous SNP.






Cluster Commands and Tricks 06/09/11

Every node has 8 cores 16GB of RAM

Useful Commands for the cluster:

List Queues and times of execution

scontrol show partitions

List Jobs


Cancel Job (jobid)

scancel -v 179

List nodes status


Submit a process

srun -p long|medium|shot| -w veredas17 -o output_file COMMAND
Example of a command:
srun -p medium -o piccard java -jar ../../bin/picard-tools-1.52/SamFormatConverter.jar INPUT=../alignment/aln.sam OUTPUT=exome.bam VALIDATION_STRINGENCY=LENIENT TMP_DIR=/tmp