format genotyping

[Jordi-V]

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

[Jordi-V]

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:

/apps/GAP2SEQ/SRC/Gap2Seq/build/Gap2Seq --vcf insertions_filtered.vcf -t 1 --reference genome.fa --filled genome.fill.fa --reads insilico3_1.fq.gz,insilico3_2.fq.gz

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??

Thanks for your time

Jordi