Question: data comparison contained in two separate vcf files
0
gravatar for nour.hadjz
4 months 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 • 167 views
ADD COMMENTlink written 4 months 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 months ago • written 4 months ago by RamRS17k
2

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

ADD REPLYlink modified 4 months ago • written 4 months ago by cpad01129.0k
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