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script for filtering swapped sites. #2

Merged
merged 4 commits into from
Mar 12, 2019
Merged

script for filtering swapped sites. #2

merged 4 commits into from
Mar 12, 2019

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yfarjoun
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gbggrant
gbggrant approved these changes Mar 12, 2019
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👍

ArraysAmbiguousSNPMiscallingMar2019/filter_vcf.sh
echo "indexing vcf"
$GATK IndexFeatureFile -F $VCF 2> index.vcf.log || (cat index.vcf.log && exit 1)

echo "grabbing dictionary from interval list"
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Maybe there's a tool for this? Didn't realize it was as simple as that.

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there's no tool since this is a bad usecase...we should be able to use interval_lists as masks in GATK...but they need a tribble codec broadinstitute/gatk#5788

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once we go to bed, we are not sure that the dictionaries match...so I had to extract it by hand...

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actually...it doesn't do what I want...:-(

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oh well.

@yfarjoun yfarjoun merged commit d9ec006 into master Mar 12, 2019
@yfarjoun yfarjoun deleted the yf_filter_script branch March 12, 2019 22:49
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@gbggrant gbggrant gbggrant approved these changes

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@yfarjoun @gbggrant