Identifying unique SNPs between species

Question

[Wilber0x]

I have 8 samples each with a VCF file made from aligning a genome skim of that sample to the same reference. I can see the number of SNPs for each sample in their individual VCF files, but I want to know how many SNPs and which SNPs are unique to each sample.

Can I merge the VCF files into one to do this? If so how?

I used bowtie2 for the alignment.

Answer 1

[guillaume.rbt]

I've dealed with the same type of analysis.

My solution was to do a pooled genotyping thanks to the GATK "best practices" pipeline, to obtain a single multi-sample VCF with the called genotypes of all my samples.

Then I filtered this VCF to obtain SNPs unique to each sample, for that you can use "SnpSift filter". (http://snpeff.sourceforge.net/SnpSift.html#filter), with the isVariant() and isRef() functions.

Answer 2

[finswimmer]

Merging is a good idea. You can do it like this:

1. bgzip all vcf files

$ parallel bgzip -c {} > {}.gz ::: *.vcf

2. tabix index these files

$ parallel tabix {} ::: *.vcf.gz

3. create a list of compressed vcf files

$ find -maxdepth 1 -iname "*.vcf.gz" > samples.txt

4. merge files, normalize and split multiallelic variants

$ bcftools merge -l samples.txt -Ou | bcftools norm -f ref.fa -m - -o merged.vcf

5. filter merge vcf file for sites, where only one sample has at least one ALT allele and create a new vcf file for each sample with its private variants

$ parallel "bcftools view -i 'COUNT(GT=\"alt\") = 1' merged.vcf | bcftools view -x -s {} -o {}.privat.vcf" ::: `bcftools query -l merged.vcf`