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abyzovlab / CNVpytor

a python extension of CNVnator -- a tool for CNV analysis from depth-of-coverage by mapped reads
MIT License
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Interpret genotype output #153

Closed sophie-03 closed 10 months ago

sophie-03 commented 1 year ago

I have successfully called CNVs from my samples and have run the following command to genotype my calls: awk '{ print $2 }' calls.1000.tsv | cnvpytor -root GTEX.pytor -genotype 1000 -a > genotypes.tsv

This has given me the following output:

chr1:1-10000    0.0000  0.000000e+00    0.000000e+00    0.0000  1.0000  0       1.0000  0       0       0.0000  1.000000e+00
chr1:54001-58000        0.5953  1.496377e+02    4.834292e-23    0.5821  0.0000  44100   1.0000  0       0       0.0000  1.000000e+00
chr1:60001-64000        0.7412  5.057931e+01    2.713928e-15    0.5799  0.0000  50100   1.0000  0       0       0.0000  1.000000e+00
chr1:72001-92000        0.5996  3.860356e-07    7.547047e-25    0.8935  0.0000  62100   1.0000  0       0       0.0000  1.000000e+00

From this, how can I determine the genotype (homozygous, heterozygous)?

Looking at a response to a previous issue, I can see that genotype can be worked out from the BAF likelihood. However in my output the BAF likelihood (column 11) is 0 for all of the CNVs in this sample.

Thanks in advance for your help.

arpanda commented 1 year ago

Looks like both all for sites doesn't have a snps (column 9 and column 10 ) ref.

did you run the -snps related steps to import the variant informations ?

-Arijit