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Ignore sites with null GTs during de novo rate calculation #810

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Ignore sites with null GTs during de novo rate calculation #810

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b565e7e
keep nulls for fam qc
epiercehoffman May 5, 2025
6c5590d
fix column number
epiercehoffman May 9, 2025
7dcbabb
drop null gts in per-sample benchmarking
epiercehoffman May 22, 2025
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2 changes: 1 addition & 1 deletion src/sv-pipeline/scripts/vcf_qc/collectQC.perSample_benchmarking.sh
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Expand Up @@ -155,7 +155,7 @@ while read ID; do
if [ ! -z ${VIDlist} ] && [ -s ${VIDlist} ]; then
echo $ID
zcat ${VCFSTATS} | head -n1 > ${OVRTMP}/SET1_calls/${ID}.SET1.SV_calls.bed
zcat ${VIDlist} | cut -f1 | fgrep -wf - <( zcat ${VCFSTATS} ) >> ${OVRTMP}/SET1_calls/${ID}.SET1.SV_calls.bed
zcat ${VIDlist} | awk '$2 != "./." {print $1}' | fgrep -wf - <( zcat ${VCFSTATS} ) >> ${OVRTMP}/SET1_calls/${ID}.SET1.SV_calls.bed
bgzip -f ${OVRTMP}/SET1_calls/${ID}.SET1.SV_calls.bed
rm -f ${OVRTMP}/SET1_calls/${ID}.SET1.SV_calls.bed
tabix -f ${OVRTMP}/SET1_calls/${ID}.SET1.SV_calls.bed.gz
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4 changes: 2 additions & 2 deletions wdl/CollectQcPerSample.wdl
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Expand Up @@ -102,14 +102,14 @@ task CollectVidsPerSample {
| bcftools view -i 'SVTYPE=="CNV" || AC>0' \
| bcftools query -f '[%SAMPLE\t%ID\t%ALT\t%GT\t%GQ\t%CN\t%CNQ\n]' \
| awk '{OFS="\t"; gt = $4; gq = $5; if ($3 == "<CNV>") { gq = $7; if ($6 == 2) { gt = "0/0" } else if ($6 == 1 || $6 == 3) { gt = "0/1" } else { gt = "1/1"} }; print $1, $2, gt, gq}' \
| awk -v outprefix="~{outdirprefix}" '$3 != "0/0" && $3 != "./." {OFS="\t"; print $2, $3, $4 >> outprefix"/"$1".VIDs_genotypes.txt" }'
| awk -v outprefix="~{outdirprefix}" '$3 != "0/0" {OFS="\t"; print $2, $3, $4 >> outprefix"/"$1".VIDs_genotypes.txt" }'
else
bcftools view -S ~{samples_list} ~{vcf} \
| bcftools +fill-tags -- -t AC \
| bcftools view -i 'SVTYPE=="CNV" || AC>0' \
| bcftools query -f '[%SAMPLE\t%ID\t%ALT\t%GT\t%GQ\n]' \
| awk '{OFS="\t"; gt = $4; gq = $5; if ($3 ~ /CN0/) { if ($4 == "0/2") { gt = "0/0" } else if ($4 == "0/1" || $4 == "0/3") { gt = "0/1" } else { gt = "1/1"} }; print $1, $2, gt, gq}' \
| awk -v outprefix="~{outdirprefix}" '$3 != "0/0" && $3 != "./." {OFS="\t"; print $2, $3, $4 >> outprefix"/"$1".VIDs_genotypes.txt" }'
| awk -v outprefix="~{outdirprefix}" '$3 != "0/0" {OFS="\t"; print $2, $3, $4 >> outprefix"/"$1".VIDs_genotypes.txt" }'
fi

# Gzip all output lists
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6 changes: 4 additions & 2 deletions wdl/MainVcfQc.wdl
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Expand Up @@ -512,12 +512,14 @@ task PlotQcPerSample {
# Make per-sample directory
mkdir ~{prefix}_perSample/

# Untar per-sample VID lists
# Untar per-sample VID lists and exclude null genotypes
mkdir tmp_untar/
tar -xvzf ~{per_sample_tarball} \
--directory tmp_untar/
find tmp_untar/ -name "*.VIDs_genotypes.txt.gz" | while read FILE; do
mv $FILE ~{prefix}_perSample/
bname=$(basename $FILE)
zcat $FILE | awk '$2 != "./."' | gzip -f > ~{prefix}_perSample/$bname
rm $FILE
done

# Plot per-sample distributions
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