All chromosomes except chromosome 1 are LowPratio on the AGGREGATED model for DEL

[YiBenqiu]

Hi, I'm having some problems with the call SV process, here are my steps：

step1(for all samples):    ${MANTA_INSTALL_PATH}/bin/configManta.py \
    --bam ${input}/${bamsample}.mkdup.bam \
    --referenceFasta $ref \
    --runDir ${MANTA_ANALYSIS_PATH} \
    --callRegions $region (for all samples)

step2(for all samples): ${MANTA_ANALYSIS_PATH}/runWorkflow.py -j 24 (for all samples)(for all samples)

step3(for all samples): vcffilter -f "FILTER = PASS" ${sample}/results/variants/diploidSV.vcf.gz | bgzip -c > ${sample}/results/variants/diploidSV_PASS.vcf.gz (for all samples)(for all samples)

step4(for all samples): /public/home/*/manta_v1.6/libexec/convertInversion.py /usr/bin/samtools ref.toplevel.fa ${sample}/results/variants/diploidSV_PASS.vcf.gz | bgzip -c > ${sample}/results/variants/diploidSV_PASS_convertInversion.vcf.gz (for all samples)

step5: svimmer input_vcfs --threads 22 seq 1 18X Y MT | bgzip -c > merged.vcf.gz
(Since the previous step of convertInversion.py turns the INV with position 1 on some chromosomes to start from 0, there is a WARNING )
warning: [W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
Warning: Contig 'MT' was not found in file ${sample}/results/variants/diploidSV_PASS_convertInversion.vcf.gz!

step6: graphtyper genotype_sv $ref $vcf --sams=$BAMLIST --region=$chr:1-${end} --avg_cov_by_readlen=$AVG_COV --log=chr$chr.log --verbose --threads=48

step7:echo {1..18} X Y MT | tr ' ' '\n' | while read chrom; do if [[ ! -d sv_results/${chrom} ]]; then continue; fi; find sv_results/${chrom} -name "*.vcf.gz" | sort >> vcf_file_list; done

step8: bcftools concat --naive --file-list vcf_file_list -Oz -o raw_mergedSV.vcf.gz

step9: vcffilter -f "SVTYPE = DEL & SVMODEL = AGGREGATED" raw_mergedSV.vcf.gz | bgzip -c > DEL_AGGREGATED.vcf.gz

and the output file:

toy.txt