Retain reads with 0 (zero) mapping quality
I want to know how to retain reads with zero mapping quality to be carried into the next step… Im using Map with BWA-MEM followed by samtools mpileup and varscan. I want my final output to have all variants, including the ones with multiple hits, as I am studying pseudogenes. Don't know any coding, could anyone can help me do this on galaxy, please!
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crystalclear58 •
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If you specifically need help to do this on Galaxy then I suggest you post this on Galaxy help forum.
Edit: I guess you already had done so :-)