Results for "Variant calling"
Bio-Scripts
...eads in a HiSeqX Illumina Basecalling directory into various catego...sequencing data. CollectVariantCallingMetrics (Picard)...---------------------- Short Variant Discovery:...Tools that perform variant calling and genotyping for short vari...2065 days ago
- library(vcfR) # Input the files. vcf
2050 days ago
Installing Platypus on Ubuntu !
(py27) ➜ Tools git:(master) ✗ git clone https://github.com/andyrimmer/Platypus.git...inux-x86_64-2.7/fastafile.so cythoning cython/variant.pyx to cython/variant.c /home/urbe/anaconda3/envs/...ux-x86_64-2.7/cpopulation.so cythoning cython/variant...2009 days ago
Samtools commands for bioinformatician !
...bam.bam ### identifying genome variants (mpileup command) # -g : ou...d.bam.bam > sal_vars.bcf ### calling snp and indels # -c : find snp # -v : output only potential variants bcftools view -c -v sal_var...rrent version and commands ### calling snp and indels with no freque...1593 days ago
Corona variant calling steps !
#!/bin/bash FILE_PATH="data/trimmed_fastq_small/" find "$FILE_PATH" -name "*.fasta" | while IFS=...cf.gz tabix -p vcf results/bcf/$basename.vcf.gz done mkdir "Variant_Results" cp -r results/bcf/*.vcf Variant...1035 days ago
- #GATK is a toolkit developed by the broad institute focused primarily on variant discovery and genotyping. It is open source, hosted on github, and available under a BSD 3-clause license. Fi...
801 days ago
