Open zainabae opened 2 months ago
Hi, Currently, there is no option for VCF-formatted output for merged results.
Thank you, Arijit
how to obtain output vcf file using a single command like:
cnvpytor -root file.pytor -call 1000 10000 100000
?
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
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
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
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
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
Hello, is there any way to get a vcf file for the merged and filtered regions, instead of xlsx file?