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AstraZeneca-NGS / VarDictJava

VarDict Java port
MIT License
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Paired variant calling how to set the value of option "-k" #313

Open liuzhen51032 opened 4 years ago

liuzhen51032 commented 4 years ago

Hi! Thanks for the effort on this tool, definitely want it to work for us, and I have a question in my work. If I set the option "-k" to "0", only case was local realigned, but control weren't. The same site of multation hoth in case and control became two different. How to set the option let the control to be local realignment.

PolinaBevad commented 4 years ago

Hi @liuzhen51032!

If you use VarDictJava in somatic/paired mode, local realignment will be used for both normal and tumor samples automatically - we don't have option to disable/enable it separately for one of the cases, it can be disabled/enabled only for both cases together. By using -k 0 you will disable local realignment - so you do not need to set this option manually as by default VarDict will apply local realignment without -k.

Can you run the command without -k and check the result? And if it will not be realigned - can you please provide example of the command how you run paired calling at the moment?