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Compare SNP callers #5

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hollygene opened this issue Mar 22, 2021 · 4 comments

Projects

Owner

hollygene commented Mar 22, 2021

snp-sites
SAMtools
GATK
mpileup
Strelka

Others?

hollygene created this issue from a note in E_coli_AMR (To do)

Owner Author

hollygene commented Mar 26, 2021

GATK first (compare to snp-sites)

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

Owner Author

hollygene commented Mar 26, 2021

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

Owner Author

hollygene commented Mar 26, 2021

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

Owner Author

hollygene commented Mar 26, 2021

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

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