which bcftools
export BCFTOOLS_PLUGINS=/bi/software/bcftools-1.16/plugins;
echo ${BCFTOOLS_PLUGINS}
bcftools view -e ‘CHROM~”M” || CHROM~”_” || QUAL<30 || MAX(FMT/GQ)<20 || MAX(FMT/DP)<8 || AVG(FMT/DP)<5 || (COUNT(FMT/GT="het")>10 && MAX(FMT/AD[*:1]/FMT/DP[*])<0.2) || MAX(FMT/AD[*:1]/FMT/DP[*]) < 0.1’ /bi/8.xuxiong/EQA2022/20221019/All.raw.vcf.gz | less -S `
bcftools view -i ‘N_ALT=1 & AVG(FMT/DP)>8 & MIN(FMT/DP)>5 & MIN(FMT/GQ)>15 & QUAL > 30 & MAX(FORMAT/AD[*:1]/FORMAT/DP[*]) > 0.1 ‘ /bi/8.xuxiong/EQA2022/20221019/All.raw.QCflt.vcf.gz | less -S
bcftools isec /bi/8.xuxiong/EQA2022/20221019/All.raw.QCflt.vcf.gz /bi/8.xuxiong/work/WES/CYP21A2_CYP21A1P_SMN1_SMN2_HBA1_HBA2_diff.vcf.gz -n =2 -w 1 -Oz -o /bi/8.xuxiong/EQA2022/20221019/All.sp.homologous.vcf.gz ; tabix -fp vcf /bi/8.xuxiong/EQA2022/20221019/All.sp.homologous.vcf.gz ;
bcftools isec /bi/8.xuxiong/EQA2022/20221019/All.raw.QCflt.vcf.gz /bi/8.xuxiong/work/WES/CYP21A2_CYP21A1P_SMN1_SMN2_HBA1_HBA2_diff.vcf.gz -n ~10 -w 1 -Oz -o /bi/8.xuxiong/EQA2022/20221019/All.sp.nonHomo.vcf.gz; tabix -fp vcf /bi/8.xuxiong/EQA2022/20221019/All.sp.nonHomo.vcf.gz;
bcftools isec -n~10 -c none -w 1 /bi/8.xuxiong/EQA2022/20221019/All.vt.vcf.gz /bi/8.xuxiong/database/Variants.with.local.blacklist.V20211010.vcf.gz -Oz -o All.blacklist.QCflt.vcf.gz; tabix -fp vcf All.blacklist.QCflt.vcf.gz;
bcftools view -Ov -i ‘(AF>=0.5 && AN>=12) || (AF>=0.2 && AN>=30) || (AF>=0.1 && AN>=100)’ /bi/8.xuxiong/EQA2022/20221019/All.blacklist.QCflt.vcf.gz -Oz -o All.blacklist.QCflt.Batch_common.vcf.gz; tabix -fp vcf All.blacklist.QCflt.Batch_common.vcf.gz;
bcftools +split-vep -S /bi/database/VEPseverity.txt -s all:synonymous_variant+ -x /bi/8.xuxiong/EQA2022/20221019/All.vep.vcf -Oz -o All.MoreSeverity.vcf.gz; tabix -fp vcf All.MoreSeverity.vcf.gz;
bcftools +split-vep -S /bi/database/VEPseverity.txt -s all:coding_sequence_variant- -x /bi/8.xuxiong/EQA2022/20221019/All.vep.vcf -Oz -o All.modifier.vcf.gz; tabix -fp vcf All.modifier.vcf.gz;
bcftools isec /bi/8.xuxiong/EQA2022/20221019/All.sp.nonHomo.vcf.gz /bi/8.xuxiong/database/ClinVar.HGMD.Local.SpliceAI.whitelist.V20211010.vcf.gz -n =2 -w 1 -Ov | less -S
bcftools concat -a /bi/8.xuxiong/EQA2022/20221019/All.sp.homologous.vcf.gz /bi/8.xuxiong/EQA2022/20221019/All.sp.nonHomo.vcf.gz -Ov|less -S
bcftools +split /bi/8.xuxiong/EQA2022/20221019/All.vep.flt.vcf -Ov -o . -G pedGroupsVEP.tsv;
bcftools query -l /bi/8.xuxiong/EQA2022/20221019/All.vep.flt.vcf | bcftools +split -S /dev/stdin -Oz -o . /bi/8.xuxiong/EQA2022/20221019/All.vep.flt.vcf
bcftools annotate -a /bi/database/gene_region.bed.gz -c CHROM,FROM,TO,GENE -H ‘##INFO=<id=gene,number=1,type=string,description="gene less=""></id=gene,number=1,type=string,description="gene>
bcftools annotate -a /bi/database/gene_region.bed.gz -c CHROM,FROM,TO,GENE -H ‘##INFO=<id=gene,number=1,type=string,description="gene bcftools="" query="" -f="" less=""></id=gene,number=1,type=string,description="gene>
bcftools +fill-tags All.raw.QCflt.vcf — -t FORMAT/VAF |bcftools query -H -f ‘%CHROM\t%POS\t%REF\t%ALT[\t%VAF]\n’|less -S
(bcftools +fill-tags /bi/8.xuxiong/EQA2022/20221019/All.sp.nonHomo.flt.vcf.gz — -t FORMAT/VAF |bcftools query -H -f ‘[\t%VAF]\n’|head -n 1|perl -ne ‘s/^#\s*|[\d+]|:VAF//g;print “chr\tstart\tend\tallele\t$_”;’; \ bcftools +fill-tags /bi/8.xuxiong/EQA2022/20221019/All.sp.nonHomo.flt.vcf.gz — -t FORMAT/VAF |bcftools query -f ‘%CHROM\t%POS\t%END\t%REF/%ALT[\t%VAF]\n’) | less -S
bcftools view -s WES22070248.bam /bi/8.xuxiong/EQA2022/20221019/All.vep.flt.vcf|less -S
bcftools view -s WES22070248.bam /bi/8.xuxiong/EQA2022/20221019/All.vep.flt.vcf|bcftools view -e ‘FMT/GT[0]==”RR” || FMT/GT[0]==”mis”‘ | bcftools annotate -x ^INFO/CSQ |bcftools norm -d none|less -S
bcftools query -l /bi/8.xuxiong/EQA2022/20221019/All.vep.flt.vcf
bcftools annotate —set-id ‘%CHROM-%POS-%REF-%FIRST_ALT’ /bi/8.xuxiong/EQA2022/20221019/All.raw.QCflt.vcf|less -S bcftools annotate —set-id +’%CHROM-%POS-%REF-%FIRST_ALT’ /bi/8.xuxiong/EQA2022/20221019/All.raw.QCflt.vcf|less -S
bcftools annotate -x ^INFO/AF,^INFO/AC,^INFO/AN /bi/8.xuxiong/EQA2022/20221019/All.raw.QCflt.vcf|less -S
zcat ~/data/database/2021Q4/HGMD_Pro_2021.4_hg19.vcf.gz | \ awk ‘/^##contig/ {next} /^#CHROM/ {printf(“##contig= bcftools annotate —rename-chrs /bi/database/chr-names.txt -x ^INFO/CLASS | \ bcftools query -f “%CHROM\t%POS\t%ID\t%REF\t%ALT\t%QUAL\t%FILTER\t%INFO/CLASS\n”| \ awk -F”\t” ‘{print $NF}’|sort|uniq -c