Everything here looks good, except that I'd expect the INFO field to read "AF=0.2,0.1;MAF=0.2;TYPE=INDEL" Even a multiallelic variant only has a single MAF: it's the allele frequency of the second most common allele. But the fill-tags plugin computes the MAF as if I had given this...
bcftools +fill-tags Extend generalized functions so thatFORMATtags can be filled as well, for example: bcftools +fill-tags in.bcf -o out.bcf -- -t 'FORMAT/DP:1=int(smpl_sum(FORMAT/AD))' Allow multiple custom functions in a single run. Previously the program would silently go with the...
计算每个样本每个位点的VAF,并转成tsv格式 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 ...
List item I tried adding the F_MISSING tag using bcftools 1.16. When I run this command: bcftools +fill-tags input.vcf.gz -- -t 'F_MISSING' | bcftools view -i 'INFO/F_MISSING<0.25' -Oz -o output... snakemake bcftools ra23mik 11...
fill-AN-AC.so /usr/lib/arm-linux-gnueabihf/bcftools/fill-from-fasta.so /usr/lib/arm-linux-gnueabihf/bcftools/fill-tags.so /usr/lib/arm-linux-gnueabihf/bcftools/fixploidy.so /usr/lib/arm-linux-gnueabihf/bcftools/fixref.so /usr/lib/arm-linux-gnueabihf/bcftools/frameshifts.so /usr/lib/arm...
...$ bcftools view -i 'GT="alt" & FORMAT/AD[:1]/FORMAT/DP>0.2' -H one_sample.vcf.gz | wc -l 61825 $ bcftools...在计算方面,bcftools通过plugin对此提供了支持,fill-tags for DP[3]。...' # bcftools=1.15测试 $ bcftools query -f '[%CHROM\_%POS\_%REF\_%ALT %SAMPLE %GT %DP...
Extend generalized functions in fill-tags more Jun 16, 2021 gvcf.c Check return status of all *write() and *close() calls Jul 20, 2018 gvcf.h Bringing "call --gvcf" from experimental to main repo. Sep 30, 2015 hclust.c Use #include <assert.h> in source files that use assert() ...
bcftools +fill-tags: Added new annotations:INFO/END,TYPE,F_MISSING. bcftools filter: Make--SnpGapoptionally filter also SNPs close to other variant types. (#1126) bcftools gtcheck: Complete revamp of the command. The new version is faster and allows N:M sample comparisons, not just 1:N ...
6 返回的数组 CSS： 1 #havetags span, 2 #addtags span { 3 display: inline-block;...
test fill-tags: added prefix test case 6 years ago .gitattributes Travis builds clone corresponding htslib branch 7 years ago .gitignore add test/test-regidx to .gitignore [minor] 6 years ago .travis.yml test plugins via travis too 6 years ago AUTHORS Added missing contributors 7 ...