bcftools mpileup -Ou -f REF.fa reads.bam | bcftools call -mv -Oz -o reads.vcf.gz -g, --gvcfINT:输出GVCF文件 -G FILE:以群体进行变异检测 4. bcftools cnv 检测拷贝数变异,输入文件为vcf文件需要BAF(B-allele frequency)和LRR(Log R Ratio)注释信息 bcftools cnv -o cnv/ test.vcf.gz 5. bc...
It contains all the vcf* commands which previously lived in the htslib repository (such as vcfcheck, vcfmerge, vcfisec, etc.) and the samtools BCF calling from bcftools subdirectory of samtools. For a full documentation, see bcftools GitHub page. Other useful links: File format specifications ...
merge add support for merging FORMAT strings bug fixed in gVCF merging mpileup a new optional SCR annotation for the number of soft-clipped reads reheader new -f, --fai option for updating contig lines in the VCF header +trio-stats extend output to include DNM homs and recurrent DNMs...
gvcf.h Bringing "call --gvcf" from experimental to main repo. 9年前 hclust.c gtcheck: prevent segfault with positive values of-c max 9年前 hclust.h gtcheck: improved cross-check mode 9年前 hex.h Update variantkey with the new header-only version ...
bcftools继续分析20%的数据,但它总是过早地终止,只为一部分变体(从200万个细菌基因组中产生高达500 2M )产生一个合并的bcf文件。我使用的代码如下:bcftools1.7/bcftoolsmerge -l VarList.txt -0 --missing-to-ref --threads 1 -O b > CombinedVCF输出错...
It contains all the vcf* commands which previously lived in the htslib repository (such as vcfcheck, vcfmerge, vcfisec, etc.) and the samtools BCF calling from bcftools subdirectory of samtools. For a full documentation, see bcftools GitHub page. Other useful links: File format specifications ...
bcftools merge gvcf unexpected output needs-feedback requires-test-case #1940 opened Jun 8, 2023 by juliagrp 1 fill-tags issue for specific sample name requires-test-case #1933 opened May 31, 2023 by huangl07 3 fill-tags plugin bug for special sample names requires-test-case #19...
gvcf.o: gvcf.c $(gvcf_h) $(bcftools_h) kmin.o: kmin.c kmin.h @@ -283,6 +287,7 @@ mpileup.o: mpileup.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(hts bam2bcf.o: bam2bcf.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_kstring_h) $(htslib_kfunc_...
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() Feb 20, 2020 hclust.h gtcheck: improved cross-check mode Au...
vcfcall: gvcf calling not working with -c calling mode yet 7 years ago consensus.c Clarified usage of consensus, resolves samtools#480 6 years ago convert.c convert: use the new kputd from htslib 5 years ago convert.h Speedup of bcftools query when FORMAT fields are not printed...