Description
These tracks contain information about short indels variations in several Saccharomyces cerevisiae strains of the Peterhof genetic collection.
For more information on strains please see the description page.
Methods
Short reads were aligned with bowtie v2.1.0; SNV calling was performed with samtools v1.0 mpileup. Only indels with quality above 30 and supported with all reads are shown. Files were annotated with SnpEff v4.1.
References
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods [Internet]. Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.; 2012 Apr;9(4):357. Available from: http://dx.doi.org/10.1038/nmeth.1923
Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin) [Internet]. Landes Bioscience; 2012 Jan 1 [cited 2014 Jul 17];6(2):80-92. Available from: https://www.landesbioscience.com/journals/fly/article/19695/
Li H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics [Internet]. 2011 Nov 1 [cited 2015 Mar 6];27(21):2987-93. Available from: http://bioinformatics.oxfordjournals.org/content/27/21/2987.long
Contacts
If you have questions please contact Polina Drozdova at p.drozdova@spbu.ru.
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