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bowtie 1 is good for short read < 50bp, how long is your read? bowtie2 is better for reads > 50 bp
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Hi!
I'm also confused by this. And the site (https://gatkforums.broadinstitute.org/gatk/categories/gatk-support-forum) is closed. Have you …
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Indeed, I thought the quality might be a factor. Still, given the information, it seems odd to me that that call was made.
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To generate a VCF file one would normally pipe the input of an `mpileup` command into an actual `call` command. For example:
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