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walaj / VariantBam

Filtering and profiling of next-generational sequencing data using region-specific rules
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nbase filter #23

Open zhoudreames opened 1 year ago

zhoudreames commented 1 year ago

image i want to exclude N >1000 reads for RNA bam files, for example, the reads "9ae8a1cd-1a71-40d1-ab06-f1567ec79f9a" contained 1593N, it should be filtered. However , this software not work when I used this code "variant GW004.ONT.RNA.sorted.filter.chr7.bam --max-nbases 1000 -o GW004.ONT.RNA.sorted.filter.chr7.N10k.bam -b -t100" This why? Thanks~

zhoudreames commented 1 year ago

by using the above code, the file size is same as the raw bam files, suggest this n-base filter is not work @chapmanb @llincoln3 @walaj I am so sorry to disturb you, can you help me?

walaj commented 1 year ago

Thanks for finding this. I found the bug and just pushed changes. Will need to update the SeqLib submodule as well, easiest would be just re-clone (recursive) VariantBam and rebuild