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I only want to know which format return the program... I ran several programs to detect de novo insertions, but I want to know if the vcf which I send is overwrite with GT information.
Thanks
Jordi
The text was updated successfully, but these errors were encountered:
Dear,
I'm so sorry but I've a new question.... I cannot run the Gap2Seq program... I try to run Gap2Seq in order to genotype a vcf which only contains insertions.... The program is Pamir and I ran the progrma like this:
the fastq files are compressed....
the error which I recive is:
Parsing VCF
Traceback (most recent call last):
File "/apps/GAP2SEQ/SRC/Gap2Seq/build/Gap2Seq", line 451, in
args['bed'], args['gaps'] = cut_vcf(args['vcf'], args['reference'], args['k'], args['fuz'])
File "/apps/GAP2SEQ/SRC/Gap2Seq/build/Gap2Seq", line 329, in cut_vcf
for line in f:
NameError: name 'f' is not defined
So Why dont detect f?? I think that f is reference genome where is included like reference_file but insted using this variable in the program we found f.... Is a bug?? How can I solve the problem? The command is well constructed? and finally all vcfs from all different programs I can use it the Gap2Seq in order to genotype the de novo insertions??
Dear,
I only want to know which format return the program... I ran several programs to detect de novo insertions, but I want to know if the vcf which I send is overwrite with GT information.
Thanks
Jordi
The text was updated successfully, but these errors were encountered: