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Old 07-05-2017, 07:06 AM   #1
MGCBrown
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Location: Canada

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Default How to extract SNPs between samples, but not between samples and reference.

Hello,

I have used samtools mpileup, and bcftools call/filter (v1.5) to call SNPs between 4 samples and a de novo reference transcriptome.

I'm interested in extracting SNPs that occur between individual samples, and not between the samples and the reference. I would like to see how different each sample is different, or similar, from one another. Is this possible? I haven't been able to find much documentation on how one would approach this.

Any info would be greatly appreciated.

Cheers.
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Old 07-05-2017, 08:43 AM   #2
lindenb
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cross posted https://www.biostars.org/p/261007/
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