What open source alignment software, variant callers are most appropriate for the whole genome experiments?
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6.9 years ago
vassialk ▴ 200

What open source alignment software, variant callers are most appropriate for the whole genome annotated to whole genome contig mutation search? I have BBMap, Bowtie, BWA and SamTools and GATK with VCF tools. Is it enough, someone knows a better pipeline?

vcf sequencing tuberculosis wgs • 1.6k views
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6.9 years ago
User 59 13k

https://github.com/chapmanb/bcbio-nextgen

And essential reading:

http://bcb.io/

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6.9 years ago

As the author of BBMap (with the associated bias), I will state that most alignment programs can identify perfectly-mapping reads or reads with 1 SNP. Once you diverge from that and are interested in areas with many substitutions or long indels, BBMap tends to have much higher sensitivity than alternatives.

I can't offer good advice on variant-callers, though.

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