Question: data comparison contained in two separate vcf files
0
gravatar for nour.hadjz
4 weeks ago by
nour.hadjz0
nour.hadjz0 wrote:

Hello !

I have 2 vcf files that each contain individuals and their genotypes. how do i compare the genotypes of the individuals contained in my first file and the genotypes of the individuals contained in my second file using dictionaries in python ?? please!

thank you for your help

code python dictionnay • 112 views
ADD COMMENTlink written 4 weeks ago by nour.hadjz0
2

Why python? Python's not a great choice for native code to parse large files. You're better off using bcftools to extract just the GT information for each sample in a 2D matrix/table (where each record is chr pos ref alt sample1_gt sample2_gt ... sampleN_gt) and using python to work on this intermediate file.

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by Ram15k
2

Try: vcf-compare -g, --cmp-genotypes from VCFtools It compares genotypes

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by cpad01126.4k
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