bcftools在筛选突变方面非常方便,给大家介绍一下,尤其是Expression的功能 更信息可参考,尤其是Expression部分 https://samtools.github.io/bcftools/bcftools.html 欢迎关注公众号,参与讨论
java -jar GenomeAnalysisTK.jar VariantFiltration -R ref.fa -V file.vcf.gz --filter-expression "QD < 2.0 || FS > 60.0 || MQ < 40.0 " --cluster-window-size 5 --cluster-size 2 --filter-name my_snp_filter -O filter.vcf.gz 注:可以先用GATK进行过滤,再使用其他软件过滤,这样无需建立索...
Newly the-c, --columnsoption can be omitted when a subfield is used in-i/-efiltering expression. Note that-cmay still have to be given when it is not possible to infer the type of the subfield. Note that this is an experimental feature. ...
Make it possible to refer to the ID column from the FORMAT expression Jan 3, 2025 convert.h Suppress printing of column indices with -H Apr 30, 2024 csq.c Change in the --unify-chr-names option Mar 19, 2025 dbuf.h New -H, --header-line option Mar 11, 2022 dist.c Changes to ...
fprintf(stderr, " -i/e, --include/--exclude <expr> select/exclude sites for which the expression is true (see man page for details)\n"); fprintf(stderr, " -k/n, --known/--novel select known/novel sites only (ID is not/is '.')\n"); ...
[bcftools] 过滤vcf #-i/e, --include/--exclude <expr> #select/exclude sites for which the expression is true (see man page for details) bcftools view -i "DP>10" -o ${vcf}.gz -Oz ${vcf} expressions 报错: Both INFO/DP and FORMAT/DP exist, which one do you want?
" -g, --group-by EXPR Group gVCF blocks according to the expression\n" " -o, --output FILE Write gVCF output to the FILE\n" " -O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n" " --write-index[=FMT] Aut...
if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n"); args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; case 'i': if ( args->filter_str ) error("Error: only one -i or -e expression can b...
a-solovyev12 pushed a commit to ebi-gene-expression-group/bioconda-recipes that referenced this issue Jun 29, 2020 [ci skip] Merge PR 21878 … d5a1f20 cdunn2001 mentioned this issue Aug 15, 2020 Update pbipa (fix build) #23956 Merged samnooij added a commit to samnooij/genomics-...
finally apply *--mark-del*, *--mark-ins*, *--mark-snv* masks [[convert]] === bcftools convert '[OPTIONS]' 'FILE' === VCF input options: *-e, --exclude* 'EXPRESSION':: exclude sites for which 'EXPRESSION' is true. For valid expressions see *<<expressions,EXPRESSIONS>>*. *-i...