vccri / vpot Goto Github PK

Hi

I am really interested in VPOT to prioritize variants. first I used the example provided (test data) it worked perfectly.

I have multiple VCF multiple patient samples, VPOT worked with two but not the third one

1. Could you please help me to figure out why it didn't work with my third vcf file ? as the error message doesn't specify couldn't upload the vcf

2. when i create test_VCF_sample_list.txt in Linux VPOT doesn't read the samples and it gives me error ; how can i overcome this issue although im checking the space and the spelling?
   error message : FileNotFoundError: [Errno 2] No such file or directory: 'PBG-653-21_S3.vcf PBG-653-21_S3'
   code used:
   [sturkistany@klogin1 project2] i = PBG-653-21_S3.vcf
   [sturkistany@klogin1 project2] j=$(echo $i | cut -f1 -d'.')
   [sturkistany@klogin1 project2]$ echo -e $i $j > test_VCF_sample_$j.txt
   [sturkistany@klogin1 project2]$ sed -i 's/\r$//g' test_VCF_sample_$j.txt
   [sturkistany@klogin1 project2]python3 ../../VPOT.py priority testout_ test_VCF_sample_$j.txt default_0.001_variants_parameters_PPF.txt
   #VPOT version 2 - 07/01/2021
   VPOT Prioritisation - Main
   Samples input files : test_VCF_sample_PBG-653-21_S3.txt
   vcf PBG-653-21_S3
   VPOT: Parameter file supplied
   QC MaxCOverage : 0
   QC Hete_balance : 0
   QC Genotype_Quality : 0
   VS Score Threshold : 0
   default_0.001_variants_parameters_PPF.txt
   Traceback (most recent call last):
   File "../../VPOT.py", line 177, in
   main()
   File "../../VPOT.py", line 135, in main
   VPOT_1_prioritise.main() #
   File "/fefs1/cegmr/sturkistany/VPOT-master/VPOT_1_prioritise.py", line 299, in main
   error=VPOT_1_1_VCF.read_variant_source_file() #
   File "/fefs1/cegmr/sturkistany/VPOT-master/VPOT_1_1_VCF.py", line 164, in read_variant_source_file
   if ( setup_for_this_src_file(this_line) != 0 ): #
   File "/fefs1/cegmr/sturkistany/VPOT-master/VPOT_1_1_VCF.py", line 268, in setup_for_this_src_file
   with open(file_line[0],'r',encoding="utf-8") as source_vcf : #
   FileNotFoundError: [Errno 2] No such file or directory: 'PBG-653-21_S3.vcf PBG-653-21_S3'

3. can i add Clinvar to the PFF parameters ? how ?

Thanks!

Hi!
I would like to use VPOT to prioritize variants in my dataset which were annotated with VEP. I have successfully run the convertVEP step, however while submitting the converted vcf into the VPOT Prioritisation step I am getting the following error:
#VPOT version 2 - 07/01/2021 VPOT Prioritisation - Main Samples input files : sample_list.tsv vcf VPOT: Parameter file supplied QC MaxCOverage : 0 QC Hete_balance : 0 QC Genotype_Quality : 0 VS Score Threshold : 0 ppf.txt processing input file : ['data.vcf', 'sample1', ''] Traceback (most recent call last): File "../VPOT.py", line 177, in <module> main() File "../VPOT.py", line 135, in main VPOT_1_prioritise.main() # File "~/VPOT/VPOT_1_prioritise.py", line 299, in main error=VPOT_1_1_VCF.read_variant_source_file() # File "~/VPOT/VPOT_1_1_VCF.py", line 178, in read_variant_source_file work_this_src_file(this_line) # File "~/VPOT/VPOT_1_1_VCF.py", line 401, in work_this_src_file work_this_src_file_1(source_vcf,wrkf1) # File "~/VPOT/VPOT_1_1_VCF.py", line 379, in work_this_src_file_1 check_this_variant(src_line, wrkf1) # File "~/VPOT/VPOT_1_1_VCF.py", line 433, in check_this_variant elif (GENOTYPE1[0] == GENOTYPE1[1]) : # a homozygous alt genotype IndexError: list index out of range

It seems that the issue arises during the parsing of sample genotypes. I would appreciate a lot any hints of how to tackle this problem!

Best,

Anastasia

Sorry, I want to use VPOT tool because I want to do variant prioritization with my data. How can I do?

Hi

I am using VPOT and its working very well except for multiple vcfs . Please see the error message below
[sturkistany@kdata1 test5]$ python3 ../VPOT.py priority testout_$vcf_f test_VCF_sample_Rabie_I_HD99_S28.txt default_0.001_variants_parameters_PPF.txt
#VPOT version 2 - 07/01/2021
VPOT Prioritisation - Main
Samples input files : test_VCF_sample_Rabie_I_HD99_S28.txt
vcf
VPOT: Parameter file supplied
QC MaxCOverage : 0
QC Hete_balance : 0
QC Genotype_Quality : 0
VS Score Threshold : 0
default_0.001_variants_parameters_PPF.txt
processing input file : ['Rabie_I_HD99_S28.vcf', 'Rabie_I_HD99_S28', '']
Traceback (most recent call last):
File "../VPOT.py", line 177, in
main()
File "../VPOT.py", line 135, in main
VPOT_1_prioritise.main() #
File "/fefs1/cegmr/sturkistany/VPOT-master/VPOT_1_prioritise.py", line 299, in main
error=VPOT_1_1_VCF.read_variant_source_file() #
File "/fefs1/cegmr/sturkistany/VPOT-master/VPOT_1_1_VCF.py", line 178, in read_variant_source_file
work_this_src_file(this_line) #
File "/fefs1/cegmr/sturkistany/VPOT-master/VPOT_1_1_VCF.py", line 401, in work_this_src_file
work_this_src_file_1(source_vcf,wrkf1) #
File "/fefs1/cegmr/sturkistany/VPOT-master/VPOT_1_1_VCF.py", line 379, in work_this_src_file_1
check_this_variant(src_line, wrkf1) #
File "/fefs1/cegmr/sturkistany/VPOT-master/VPOT_1_1_VCF.py", line 433, in check_this_variant
elif (GENOTYPE1[0] == GENOTYPE1[1]) : # a homozygous alt genotype
IndexError: list index out of range

not sure what is the problem here, Please let me know how i can overcome this?

Shereen