PRIORTIZATION about vpot HOT 5 CLOSED

Thanks for looking at our VPOT software.

When creating your input file for the VPOT priority command, you should separate the values on each line with tab characters. If you look at the example file, test_data/test_VCF_sample_list.txt, you will see that the value on each line are separated by tabs (not spaces). I will update the documentation to make this point clear.

If you wanted to do this with linux bash code, as you showed in your question, you could do this like:
vcf_f=PBG-653-21_S3.vcf
sample=${vcf_f%.vcf} # extract the filename without the .vcf extension
out_f=test_VCF_sample_${sample}.txt
echo -e "${vcf_f}\t${sample}" > $out_f
# you could add more lines to the file by using something like:
# ...similar code as above to
# echo -e "${vcf_f_2}\t${sample_2}" >> $out_f

Of course for testing purposes, you don't need to do this - you could just create your file with your preferred text editor - making sure that actual tab characters are used to separate the vcf filename & the sample name.

"can i add Clinvar to the PFF parameters ? how ?"
Yes. Using the VT section of the PPF file.

Refer to test_data/default_0.001_variants_parameters_PPF.txt - the default PPF file. You could add a line for Clinvar. E.g.
VT CLNSIG Pathogenic 200
This would score an INFO field value of CLNSIG equal to "Pathogenic" a value of 200.
NOTE - use tabs to separate values - not spaces. It will be easier to use a text editor to edit this file.
Also NOTE that the supplied test data files do not have the normal VCF annotation for Clinvar. Use your own data or modify the supplied test data so that the INFO field in the VCF contains the correct annotation (e.g. ...;CLNSIG=Pathogenic;...)

I hope this helps to move you forward testing VPOT.

from vpot.

Thanks for answering my questions !

regarding the population frequency .. PF I don't want to filter out variants.. instead i want to weight the population frequency according to ranges
for example :
ExAC_ALL less than and equal to .01 scored 100
ExAC_ALL greater than and equal to .05 scored -100
ExAC_ALL .011 - .049 scored 0

is this possible with VPOT?

from vpot.

You can use any annotation field for prioritisation determination within the PD field.
In the case of ExAC_ALL, you would set it as a numeric PD field with different scoring boundaries, like the CADD_phred PD line you see in the example PPF.
eg :

PD<tab>ExAC_ALL<tab>N<tab>0.011<100>0.5<tab>0<tab>0.5<tab>-100

You do not need to have ExAC_ALL in the PF field, or you can keep it as a bookmark with the value 1.01, so it keeps all variants.

from vpot.

Thanks it worked with me.

for me im using Annovar as annotation tool, and whenever ExAC_ALL has no value it is given (.) e.g. ExAC_ALL=.;

is there a way to weight it without replace the . with value such as -999 ?

from vpot.

Yes.

NOTE that a numeric value of "." will be treated as -999 for the PF setting. You can allow for this in your PF settings in the PPF file.

If you would like to score the "." value, you could create new PD entry like:
PD<tab>ExAC_ALL<tab>A<tab>.<tab>100
This example assigns a VPOT value of 1 to an alpha value of "." for ExAC_ALL.

You can still have another PD ExAC_ALL entry for your numeric values.

from vpot.