
Michael Gatzen
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Activity overview
Latest activity by Michael Gatzen-
Michael Gatzen commented,
And to keep you posted xinping fan, the change has been merged into master in this PR. Thank you very much again!
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Michael Gatzen commented,
Hi xinping fan, Thank you for posting this! You are totally correct, that line should be appending the RG attribute of the read (instead of the string "RG"). I will create an issue and a PR in pica...
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Michael Gatzen commented,
Hi Dong Yiyi, It is true that MarkDuplicates by default only marks the reads as duplicates and does not remove them (unless you set REMOVE_DUPLICATES to true). Every GATK tool has a default duplica...
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Michael Gatzen commented,
Hi Marcela, The command you posted should work without a problem. Is the output you posted the complete output? The last line should end with a line that says "Tool returned: 0". If it doesn't then...
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Michael Gatzen commented,
Hi Peter Braund, If I understand your question correctly, you're wondering what the purpose of TAGS_TO_DROP=MAX_AF is. You're absolutely right that TAGS_TO_REVERSE=AF will transform an AF of 0.22 t...
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Michael Gatzen commented,
Hi Sven Klages, It seems like GATK throws an error because the ML tag of a read is an empty array. The SAM spec is actually not clear about if that is allowed or not. One possibility is that the fi...
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Michael Gatzen commented,
Hi Vladimir Makarov, It is very possible that some groups at the Broad are doing feline research and have generated this resource for themselves. However, we as the developers of GATK don't distrib...
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Michael Gatzen commented,
Hi Vladimir Makarov, this is a great question! Unfortunately, we as the GATK developers don't have any resources for feline DNA. It might be worth asking in forums like https://www.biostars.org/ or...