VCF file

[zainabae]

Hello, is there any way to get a vcf file for the merged and filtered regions, instead of xlsx file?

[arpanda]

Hi,
Currently, there is no option for VCF-formatted output for merged results.

Thank you,
Arijit

[thedam]

how to obtain output vcf file using a single command like:
cnvpytor -root file.pytor -call 1000 10000 100000
?

[zainabae]

how to obtain output vcf file using a single command like:

cnvpytor -root file.pytor -call 1000 10000 100000

?

In -view mode, you can set the output file type as vcf file

> cnvpytor -root file.pytor -view 100000 
set Q0_range 0 0.5
set size_range 100000 inf
set p_range 0 0.00001
set print_filename output.vcf
print calls

[thedam]

I need to use it in pipeline, so I'd like to have somthing like this:
cnvpytor -root file.pytor -call 1000 10000 100000 -output output.vcf

[arpanda]

HI @thedam ,
Here are several approaches that can be followed to integrate into a pipeline. Below are some examples:

> echo "rdstat" | cnvpytor -root file.pytor -view 100000 -o prefix.png

> cnvpytor -root file.pytor -view 100000 <<ENDL
set Q0_range 0 0.5
set size_range 100000 inf
set p_range 0 0.00001
set print_filename output.vcf
print calls
ENDL

> cnvpytor -root file.pytor -view 100000 < script.spytor

-Arijit

[thedam]

Hi @arpanda, thanks, it works for me.

so to obtain vcf files for 1000, 10000, 100000 I have to run it three times (changing the values in bold) and then marge three vcf files?

cnvpytor -root file.pytor -view 100000 <<ENDL
set Q0_range 0 0.5
set size_range 100000 inf
set p_range 0 0.00001
set print_filename output.vcf
print calls
ENDL

[arpanda]

I would suggest to prepare separate output files. In view mode, the bin_size parameter can also be updated. Here is an example.

cnvpytor -root file.pytor -view 100000 <<ENDL
set Q0_range 0 0.5
set size_range 100000 inf
set p_range 0 0.00001
set print_filename output_100k.vcf
print calls

set bin_size 10000
set print_filename output_10k.vcf
print calls
ENDL

-Arijit