Snps Comparison
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12.2 years ago
Ric ▴ 190

Hello,

I would like to compare SNPs from different methods:

  • number of SNPs
  • SNPs postion (position where method A has SNPs but not B and vice versa. Where both have SNPs)

I would be interested to get a output file which contain all above information and also would like to see the differences visualized i.e. where could load the two files which contain the SNPs and aligment.

In which format the SNPs has to be stored and which tools have to be used in order to make a comparison possibel?

Thank you in advance.

snp bedtools gff vcftools • 3.7k views
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Do you know any programming languages? If not this could be a great opportunity to learn some perl or python.

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12.2 years ago
Mdeng ▴ 520

Hey ric,

after SNP/INDEL Calling (using samtools or GATK) your output is in VCF (Version 4.1) format. I would name VCF as the standard format for variences. For this format VCFtools offers a nice bunch of operations. E.G. the commands "vcf-isec" and "vcf-compare" should help you way out.

Also zev.kronenberg is absolutely right. This is one of the best tasks to learn a programming language. Perl could be a bit wierd for beginners, so may you wanna use python. For ruby you will find a library for parsing the vcf format here.

cheers.

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12.2 years ago
Occam ▴ 410

plink is appropriate for this. however, your data need to be plink (ped/map) format. if not in plink format, R would be good (particularly for visualization) if your data are not too large. if you have very large data, you will probably need a scripting language (perl/python). in any case, time spent learning perl/python and/or R will not be a waste of your time.

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