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hollygene / CornellPostdoc

Various scripts I used during my tenure as a Postdoctoral Associate at Cornell University
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Compare SNP callers #5

Open hollygene opened 3 years ago

hollygene commented 3 years ago

snp-sites SAMtools GATK mpileup Strelka

Others?

hollygene commented 3 years ago

GATK first (compare to snp-sites)

Code need to modify here: https://github.com/hollygene/CornellPostdoc/blob/35aa029ebd123fc28d678969465cefe5e3cef517/variantGATK.sh

hollygene commented 3 years ago

Multiple sequence alignment variant callers: SAMtools: need MSA in BAM format http://www.htslib.org/doc/samtools.html https://samtools.github.io/bcftools/bcftools.html#call

hollygene commented 3 years ago

QualitySNP software https://www.bioinformatics.nl/QualitySNPng/home.html

hollygene commented 3 years ago

Using Geneious https://help.geneious.com/hc/en-us/articles/360044627872-Can-I-call-SNPs-on-individual-sequences-aligned-to-a-reference-