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add bcftools sort step before tabix index #432

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merged 2 commits into from
Jan 20, 2022
Merged

add bcftools sort step before tabix index #432

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633700d
add bcftools sort step before tabix index to deal with different unix…
priesgo Sep 30, 2021
ea470b8
remove from the output the rawcalls.unsorted file
priesgo Sep 30, 2021
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13 changes: 7 additions & 6 deletions bin/concatenateVCFs.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -84,15 +84,16 @@ then
tail -n +$((L+1)) ${vcf}
done
done
) | bgzip -@${cpus} > rawcalls.vcf.gz
tabix rawcalls.vcf.gz
) | bgzip -@${cpus} > rawcalls.unsorted.vcf.gz
else
VCF=$(ls no_intervals*.vcf)
cp $VCF rawcalls.vcf
bgzip -@${cpus} rawcalls.vcf
tabix rawcalls.vcf.gz
cp $VCF rawcalls.unsorted.vcf
bgzip -@${cpus} rawcalls.unsorted.vcf
fi

bcftools sort rawcalls.unsorted.vcf.gz | bgzip > rawcalls.vcf.gz
tabix -p vcf rawcalls.vcf.gz

set +u

# Now we have the concatenated VCF file, check for WES/panel targets, and generate a subset if there is a BED provided
Expand All @@ -102,5 +103,5 @@ if [ ! -z ${targetBED+x} ]; then
tabix ${outputFile}.gz
else
# Rename the raw calls as WGS results
for f in rawcalls*; do mv -v $f ${outputFile}${f#rawcalls.vcf}; done
for f in rawcalls.vcf*; do mv -v $f ${outputFile}${f#rawcalls.vcf}; done
fi