Extracting specific SNPs from vcf file

Question

[konanamenanjacky]

Hello everyone, Please, I am new with bioinfo tools and I ask your help. I did GBS on two plant varieties on which I work. I have the vcf files and I want to identify SNPs that are specific to each of my varieties. Could someone point me to a program or procedure to follow? thank you so much

[konanamenanjacky]

Thank you all. I will try and keep you informed!

[konanamenanjacky]

Hello everyone, Thanks for your advice but I still have trouble sorry. Could someone help please? I tried different commands that you advised me "vcf contrast" of vcftools and "subtract" from bedtools but it does not work. Maybe I poorly explained what I want to do. I'll try to explain better. In fact I have the GBS results of my two "varieties" of plants in a single vcf file containing the SNP position on the contigs (the reference sequence is partial), genotypes and other sequencing information for all the samples. What I want is to know if some SNPs are specific to either of my two "varieties". If so, I want to identify these SNPs and extract them from the vcf file. Thanks a lot for the help.

[erikfas]

If you are able to program in Python there's a package called PyVCF, which can parse the VCF for you and giving you easy access to the genotypes for each sample. Then it would be a matter of simply filtering out those positions that are the same across all samples while keeping those that are different, and doing whatever downstream analysis you want on those.

Answer 1

[Jenez]

vcftools would probably fulfil your needs.

Answer 2

[WouterDeCoster]

Lots of filtering options are available using GATK SelectVariants:

Answer 3

[sacha]

I use variant-tools which is greate if you want to perform set operation. for instance : "Select all SNP which is not in A but in B" .

[shubhra.bhattacharya]

Hey! Can you please post an example command?

Answer 4

[Jorge Amigo]

I would also go for bedtools subtract, but if you have a single multisample vcf you first have to split it and then find the private sites:

bcftools view -m2 --samples sample1 multisample.vcf > sample1.vcf
bcftools view -m2 --samples sample2 multisample.vcf > sample2.vcf
bedtools subtract -a sample1.vcf -b sample2.vcf > sample1.private.vcf
bedtools subtract -a sample2.vcf -b sample1.vcf > sample2.private.vcf

[konanamenanjacky]

Thanks Sorry I'm not able to program in Python. I have already split my vcf file with "the commande cut" before using bedtools "subtract" but he return the following error:
commande typed: bedtools subtract -a egusi.vcf -b cal.vcf * ERROR: too many digits/characters for integer conversion in string . Exiting...

may be it is because file was split with "cut"? I will done as advised Amigo and let you know.

Thanks you so very much!

[WouterDeCoster]

You are making this thread very confusing by replying to the wrong answer with this comment, or addressing two answers simultaneously...

Answer 5

[harold.smith.tarheel]

Bedtools 'subtract' is another option.