Results for "Rare variants"
Bio-Scripts
jitendra@jitendra-UNLOCK-INSTALL[SNP] wge...read coverage to detect copy number variants. AnnotateIntervals...(BETA Tool) Calls copy-number variants in germline samples given the...ant calling and genotyping for short variants (SNPs, SNVs and Indels)...2060 days ago
Samtools commands for bioinformatician !
## count mapped reads samtools view -c -F 260 mapping_...x sal_sej_sorted.bam.bam ### identifying genome variants (mpileup command) # -g : out...els # -c : find snp # -v : output only potential variants bcftools view -c -v sal_vars...1587 days ago
Pack a perl program with their dependencies on Ubuntu !
#Follow steps to create your own executable ./web jit@jit-HP-Pro-3335-MT:~/Downl...nlocalassembly github.com - SvABA is a method for detecting structural variants in sequencing data using geno...1496 days ago
Create random 10000 SNPs in genome !
(base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -ref.... Generating the correspondance map for genomic variants introduced during simulation:...Generating reference-based vcf file for genomic variants introduced during simulation:...1195 days ago
Create random 1000 INDEL in genome !
(base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -ref.... Generating the correspondance map for genomic variants introduced during simulation:...Generating reference-based vcf file for genomic variants introduced during simulation:...1195 days ago
Create random 1000 CNVs in genome !
(base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -ref.... Generating the correspondance map for genomic variants introduced during simulation:...Generating reference-based vcf file for genomic variants introduced during simulation:...1195 days ago
Create random 5 inversions in genome !
(base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -ref.... Generating the correspondance map for genomic variants introduced during simulation:...Generating reference-based vcf file for genomic variants introduced during simulation:...1195 days ago
Create random 2 translocations in genome !
(base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -ref.... Generating the correspondance map for genomic variants introduced during simulation:...Generating reference-based vcf file for genomic variants introduced during simulation:...1195 days ago
Installing Covid19 Environment !
(base) vikas@vikas-Lenovo-ideapad-320-15ISK:~/vinodLab/Genepi$ conda env create -f...\ The default QUAST package does not include: * GRIDSS (needed for structural variants detection) * SILVA 16S rRNA...908 days ago
Install Varscan on Ubuntu / Linux !
#Varscan is a java program designed to call variants in sequencing data. It was developed at the Genome Institute at Washington University and is hosted on github. To use Varscan we simply ne...808 days ago
