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Question about creating a mask.bed file #268

@kodai-kishino

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@kodai-kishino

Based on the documentation about the necessity of a mask file and other related questions, it seems that the mask file should specify regions where reads were not mapped and variants were not called.
I attempted to generate a BED file of unmapped regions from a BAM file using bedtools complement. However, I am unsure if this is the correct approach.

bedtools complement -i smc_Pinc-p1_s.bam -g pinc_chr.genome.txt > p1_mask.bed

Thank you for your help!

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