Antonio Aleman
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Activity overview
Latest activity by Antonio Aleman-
Antonio Aleman commented,
Note: the example is ran through a Snakemake rule. Counterintuitive, I know – but we did so for benchmark automation purposes.
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Antonio Aleman created a post,
Why does the GATK-For-Microbes best-practice workflow use mutect2 instead of HaplotypeCaller?
Hey, everyone! When I use the GATK-For-Microbes workflow for variation calling, I get an erroneously high number of SNPs and indels. The issue seems to be that Mutect2 calls with an allele fraction...
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Antonio Aleman created a post,
What is a queryname? Why sort with this over coordinates?
Hey everyone! I'm new to GATK and bioinformatics and trying to use GATK for my microbial-WGS data. For the sortSam command, how do I decide between sorting by queryname or coordinates? I'm conflict...
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Antonio Aleman commented,
Might be worth updating the images on this page!
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Antonio Aleman commented,
I'm having the same issue, too. Was this ever resolved?
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Antonio Aleman created a post,
Where can I find the files for the GATK-microbe best practices?
I am trying to run the example workflow for the GATK-for-Microbes pipeline, but it cannot locate the input files in input.json. I'm assuming my wdl execution (toil) engine is suppose to download th...