README.md

How to prepare a vcf before importation SQLite db see https://github.com/tkoomar/VCFdbR for further explanation

MYVCF=Perry_truncated.vcf.gz OUTVCF=Perry_truncated_ready.vcf.gz

MYVCF=SeqOne_truncated.vcf.gz OUTVCF=SeqOne_truncated_ready.vcf.gz

This VCF needs to have all multialleleic sites split. All fields which once had one value per alternate allele (Number=A) also need to be converted to a single value (Number=1). You can do that with bcftools:

bcftools norm -c ws -f /home/ptngs/genome_references/GRCh37.fa -m - ${MYVCF} | sed -e 's/Number=A/Number=1/g' | sed -e 's/Number=./Number=1/g' | bgzip -c > TEMP.vcf.gz

bcftools view TEMP.vcf.gz | sed -e 's/Number=1,Type=Float/Number=1,Type=String/g' | sed -e 's/Number=1,Type=Integer/Number=1,Type=String/g' | bgzip -c > TEMP2.vcf.gz

if annotated_with_vep and CSQ column not be parsed correctly.

zcat TEMP2.vcf.gz| sed '/^#/! s/;;/;/g' | bgzip -c > ${OUTVCF} else mv TEMP2.vcf.gz ${OUTVCF}

tabix ${OUTVCF}

Add COSMIC annotations to vcf

file=/home/ptngs/ClinicalResultsBrowser_vcfs/SEQONE_DATABASE_EXPORTS/27_02_2023/merge_grenoble_onco.vcf.gz tmpdir=/home/ptngs/ClinicalResultsBrowser_vcfs/SEQONE_DATABASE_EXPORTS/27_02_2023/splited_onco_vcf_cosm mkdir -p ${tmpdir}/ cd ${tmpdir} VERSION=96 ID_STRING=$(echo 'cbenoit3@chu-grenoble.fr:12Azefg!' | base64) curl -H "Authorization: Basic ${ID_STRING}"
https://cancer.sanger.ac.uk/cosmic/file_download/GRCh37/cosmic/v${VERSION}/VCF/CosmicCodingMuts.vcf.gz > ${tmpdir}/url.txt URL=$(grep "url" ${tmpdir}/url.txt | sed 's/{"url":"//g' | sed 's/"}//g') curl -o ${tmpdir}/CosmicCodingMuts.vcf.gz "${URL}"

#tabix ${tmpdir}/CosmicMutantExport.tab.gz tabix -f ${tmpdir}/CosmicCodingMuts.vcf.gz bcftools query -f'%CHROM\t%POS\t%POS\t%ID\n' ${tmpdir}/CosmicCodingMuts.vcf.gz | bgzip -c > ${tmpdir}/CosmicMutantExport.tab.gz echo '##INFO=<ID=COSMIC,Number=1,Type=String,Description="Mutation Cosmic ID">' > ${tmpdir}/cosmic.hdr #tabix -f -s1 -b2 -e3 ${tmpdir}/CosmicMutantExport.tab.gz #bcftools annotate -a ${tmpdir}/CosmicMutantExport.tab.gz -h ${tmpdir}/cosmic.hdr -c CHROM,FROM,TO,ID ${file} | bgzip -c > ${tmpdir}/${file}.tmp bcftools annotate -a ${tmpdir}/CosmicMutantExport.tab.gz -h ${tmpdir}/cosmic.hdr -c CHROM,FROM,TO,INFO/COSMIC ${file} | bgzip -c > ${file}.tmp #mv ${file}.tmp ${file} cp -r ${file}.tmp ${file} tabix -f ${file}

if you vcf contains too many samples it could require to much RAM for your computer. So split it by sample like this

THREADS=2 outdir=/home/ptngs/ClinicalResultsBrowser_vcfs/SEQONE_DATABASE_EXPORTS/27_02_2023/splited_onco_vcf outdir=/home/ptngs/ClinicalResultsBrowser_vcfs/SEQONE_DATABASE_EXPORTS/27_02_2023/splited_onco_twofiles/ file=/home/ptngs/ClinicalResultsBrowser_vcfs/SEQONE_DATABASE_EXPORTS/27_02_2023/merge_grenoble_onco.vcf.gz for sample in bcftools query -l $file; do echo "bcftools view --threads ${THREADS} -Oz -s $sample -o ${outdir}/${sample}_tmp.vcf.gz $file" bcftools view --threads ${THREADS} -Oz -s ${sample} -o ${outdir}/${sample}_tmp.vcf.gz $file echo "bcftools view --threads ${THREADS} -Oz -e 'GT="./."' -o ${outdir}/${sample}.vcf.gz ${outdir}/${sample}_tmp.vcf.gz" bcftools view --threads ${THREADS} -Oz -e 'GT="./."' -o ${outdir}/${sample}.vcf.gz ${outdir}/${sample}_tmp.vcf.gz rm ${outdir}/${sample}_tmp.vcf.gz echo "tabix ${outdir}/${sample}.vcf.gz" tabix ${outdir}/${sample}.vcf.gz echo -e "\n" done

sarek vcf

cd /home/ptngs/Documents/haplotypecaller

remove Ids from vcf

bcftools annotate -x ID 23A1424_S3/23A1424_S3.haplotypecaller.filtered_VEP.ann.vcf.gz -Oz -o 23A1424_S3/23A1424_S3.haplotypecaller.filtered_VEP.ann.NoID.vcf.gz

Split multi allelic sites

bcftools norm -c ws -f /home/ptngs/genome_references/GRCh37.fa -m - 23A1424_S3/23A1424_S3.haplotypecaller.filtered_VEP.ann.NoID.vcf.gz | sed -e 's/Number=A/Number=1/g' | sed -e 's/Number=./Number=1/g' | bgzip -c > TEMP.vcf.gz bcftools view TEMP.vcf.gz | sed -e 's/Number=1,Type=Float/Number=1,Type=String/g' | sed -e 's/Number=1,Type=Integer/Number=1,Type=String/g' | bgzip -c > TEMP2.vcf.gz

format csq vep fields

zcat TEMP2.vcf.gz | sed '/^#/! s/;;/;/g' | bgzip -c > /home/ptngs/Documents/haplotypecaller/23A1424_S3/23A1424_S3.haplotypecaller.filtered_VEP.ann.NoID_splitted.vcf.gz