About inputting the type of bam file

abyzovlab / CNVpytor

a python extension of CNVnator -- a tool for CNV analysis from depth-of-coverage by mapped reads

MIT License

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About inputting the type of bam file #211

Closed oceancongliu closed 6 months ago

oceancongliu commented 6 months ago

Thanks for maintaining the software updates! I plan to analyse whole-genome sequencing data using CNVpytor software. However, should I enter the bam file from the BWA comparison or should I enter the bam file after marking duplicates using GATK.

Hope to get your answer soon, thanks!

arpanda commented 6 months ago

The BAM from BWA processing should be fine for cnvpytor input.

-Arijit