head显示前10列bcftools query -f'%POS\n'sample.vcf|head# 打印CHROM POS REF ALT 4列信息bcfto...
This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html - bcftools/mcall.c at develop · samtools/bcftools
This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html - bcftools/vcfbuf.c at develop · samtools/bcftools
Usage: samtools sort [-n] [-m <maxMem>] <in.bam> <out.prefix> -m 参数默认下是 500,000,000 即500M(不支持K,M,G等缩写)。对于处理大数据时,如果内存够用,则设置大点的值,以节约时间。 -n 设定排序方式按short reads的ID排序。默认下是按序列在fasta文件中的顺序(即header)和序列从左往右的位点...
- gap on the alt sequence between this and the next block (all but the last line) */ chain_t *chain = args->chain; int n = chain->num; int ref_end_pos = args->fa_length + chain->ori_pos; int last_block_size = ref_end_pos - chain->ref_last_block_ori; ...
- gap on the alt sequence between this and the next block (all but the last line) */ chain_t *chain = args->chain; int n = chain->num; int ref_end_pos = args->fa_length + chain->ori_pos; int last_block_size = ref_end_pos - chain->ref_last_block_ori; ...
n"; } static const char *usage_text(void) { return "\n" "About: Compare two files and set non-identical genotypes in the first file to missing.\n" "\n" "Usage: bcftools +isecGT <A.bcf> <B.bcf> [Plugin Options]\n" "Plugin options:\n" " -o, --output FILE Write output...
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error("Error: allele type not recognised. Expected one of nref|alt1|minor|major|nonmajor, got \"%s\".\n", atype_string); } } static void usage(args_t *args) { fprintf(stderr, "\n"); fprintf(stderr, "About: VCF/BCF conversion, view, subset and filter VCF/BCF files....
// output REF=CAGAGAGAGA, ALT=CAGAGAGAGAGA where REF=C,ALT=CGA could be // used. This filter is therefore more strict and may remove some valid // SNPs. int len = 1; if ( var_type & VCF_INDEL ) { for (i=1; i<line->n_allele; i++) ...