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CreateIntervalFiles #358

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v-mahughes opened this issue Oct 18, 2023 · 1 comment
Open

CreateIntervalFiles #358

v-mahughes opened this issue Oct 18, 2023 · 1 comment

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@v-mahughes
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Can you please point me to the non-autosome-sequences in this dict, and how you would pass those keys as input into the CreateIntervalFiles function? DO you add the --NON_AUTOSOME_SEQUENCE flag multiple times, with one key per flag? or do you pass all strings to a single flag? Please let me know! My hg19 ref dict is attached (changed the name from hg19.dict to hg19.txt because .dict is not a supported file type on github)

hg19.txt
@alecw
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alecw commented Oct 18, 2023 •
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HUMAN_X, HUMAN_Y and HUMAN_MT are non-autosomes. Yes, you should specify

--NON_AUTOSOME_SEQUENCE <sequence>

separately for each non-autosome sequence.

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@alecw @v-mahughes