bcftools view -S samplelistname.txt ALL.genotypes.vcf.gz -Ov > samplelist_1000Genomes.vcf 3. 将多个样本vcf文件合并成一个vcf矩阵 #将vcf进行压缩 bgzip -c -f f_nist_1_2.vcf > f_nist_1_2.vcf.gz #为VCF文件建立index bcftools index f_nist_1_2.vcf.gz # 合并SNP文件 bcftools merge fc...
vcfcall.c vcfcnv.c vcfconcat.c vcfconvert.c vcffilter.c vcfgtcheck.c vcfindex.c vcfisec.c vcfmerge.c vcfnorm.c vcfplugin.c vcfquery.c vcfroh.c vcfsom.c vcfsort.c vcfstats.c vcfview.c vcmp.c vcmp.h version.c version.shBreadcrumbs bcftools/...
$ bcftools view -cvNg abc.bcf > snp_indel.vcf 生成的结果文件为vcf格式,有10列,分别是:1 参考序列名;2 varianti所在的left-most位置;3 variant的ID(默认未设置,用’.'表示);4 参考序列的allele;5 variant的allele(有多个alleles,则用’,'分隔);6 variant/reference QUALity;7 FILTers applied;8 varian...
vcfindex.c Clarify the meaning of the --threads option. 5年前 vcfisec.c Merge pull request #1057 from jmarshall/diagnostics 5年前 vcfmerge.c More 64 bit preparations 5年前 vcfnorm.c Makebcftools normrealignment truly case insensitive. Fixes #1114 ...
vcfcall.c vcfcall: gvcf calling not working with -c calling mode yet October 1, 2015 09:29 vcfcnv.c cnv: Prior on CN2; changed the default -P to be more strict (0.5) July 7, 2015 10:29 vcfconcat.c bcf_hdr_combine replaced by bcf_hdr_merge July 6, 2015 16:47 vcf...
#include <htslib/vcf.h> #include <htslib/synced_bcf_reader.h> #include <htslib/vcfutils.h> #include "bcftools.h" #include "filter.h" #include "rbuf.h" // Logic of the filters: include or exclude sites which match the filters?#...
path.join(scratch, "tpfn", "0000.vcf.gz")), "fn") fpcounts = parseStats(runBcftools("stats", fppath), "fp") ambicounts = parseStats(runBcftools("stats", ambipath), "ambi") unkcounts = parseStats(runBcftools("stats", unkpath), "unk") res = pandas.merge(truthcounts, query...
plot-vcfstats: Open stats file in text mode, not binary (#618). fixrefplugin: Allow multiallelic sites in the-i, --use-id reference. Also flip genotypes, not just REF/ALT! merge: fix gVCF merge bug when last record on a chromosome opened a gVCF block (#616) ...
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int copy_string_field(char *src, int isrc, int src_len, kstring_t *dst, int idst); // see vcfmerge.c static void merge_info_string(args_t *args, bcf1_t **lines, int nlines, bcf_info_t *info, bcf1_t *dst) { const char *tag = bcf_hdr_int2id(args->hdr,BCF_DT_...