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Refactor merge_sv_calls.R #81

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lsantuari opened this issue Nov 30, 2020 · 1 comment
Open

Refactor merge_sv_calls.R #81

lsantuari opened this issue Nov 30, 2020 · 1 comment
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@arnikz
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0.1.0

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@lsantuari
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merge_sv_calls.R takes the output of seqkit as input
@lsantuari lsantuari added the code label Nov 30, 2020
@lsantuari lsantuari added this to the 0.1.0 milestone Nov 30, 2020
@lsantuari lsantuari mentioned this issue Nov 30, 2020
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@arnikz
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arnikz commented Nov 30, 2020 •
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merge_sv_calls.R takes the output of seqkit as input

That's correct.

sv-channels/run.sh

Line 86 in 6669847

cmd="$p locate -i -P -r -p "N+" --bed \"$FASTA\" -o \"$REF_REG\""

sv-channels/run.sh

Lines 300 to 305 in 6669847

cmd="$p.R \
-i \"$sv_dir\" \
-f \"$EXCL_LIST\" \
-n \"$REF_REG\" \
-m $c \
-o \"$bedpe\""

Could you add some details on what needs to be changed or refactored here?

@lsantuari lsantuari pinned this issue Dec 1, 2020
@lsantuari lsantuari unpinned this issue Dec 1, 2020
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