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fix: mehari wrapper vcf preprocessing does not actually fix info svlen header (#450) #451

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merged 2 commits into from
Oct 11, 2023
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fix: mehari wrapper vcf preprocessing does not actually fix info svlen header (#450) #451

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687c70d
Fix: #450 perform preprocessing on sorted vcf files
Nicolai-vKuegelgen Oct 11, 2023
63dd518
uncommenting trap of TMPDIR
Nicolai-vKuegelgen Oct 11, 2023
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4 changes: 2 additions & 2 deletions snappy_wrappers/wrappers/mehari/annotate_strucvars/wrapper.py
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Original file line number Diff line number Diff line change
Expand Up @@ -81,9 +81,9 @@
bcftools sort -o $TMPDIR/fixed_bnd_to_inv.$num.vcf $TMPDIR/fixed_bnd_to_inv_unsorted.$num.vcf

# Fixup SVLEN=1 to SVLEN=.
sed -i -e 's/ID=SVLEN,Number=1/ID=SVLEN,Number=./g' $TMPDIR/fixed_bnd_to_inv_unsorted.$num.vcf
sed -i -e 's/ID=SVLEN,Number=1/ID=SVLEN,Number=./g' $TMPDIR/fixed_bnd_to_inv.$num.vcf
# Fixup MELT header
sed -i -e "s/seperated by '..'/separated by '\\\\\\\\|'/" $TMPDIR/fixed_bnd_to_inv_unsorted.$num.vcf
sed -i -e "s/seperated by '..'/separated by '\\\\\\\\|'/" $TMPDIR/fixed_bnd_to_inv.$num.vcf

# Add the missing "GT" tag
echo '##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">' \
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