使用bcftools query -l test.vcf > 453.list 将vcf文件中的样品名提取出来 不使用软件：head -100 all.vcf |grep "#C" |cut -f10-|xargs -n 1 > wild.txt 使用sh脚本 将453份数据写入变量$sample for sample in $(cat 453.list);创建每个样本的list文件 do to...
|gzip - > clean.vcf.gz这一步输出的vcf.gz文件，用 bcftools query -l clean.vcf.gz | wc -l...
(FORMAT/DP)<5' | bcftools query -l | wc -l) echo "scale=5; $nSites_DPfilter / $nSites_unfiltered" | bc #0.17349 - sites are removed, even though the filter is being applied to samples echo "scale=5; $nSamples_DPfilter / $nSamples_unfiltered" | bc #1.00000 - no samples ...
Also note the INSTALL notes give hints how you can avoid LD_LIBRARY_PATH if you wish. Eg via: ./configure CPPFLAGS=-I/my_home/root/include \ LDFLAGS='-L/my_home/root/lib -Wl,-R/my_home/root/lib' Author
从vcf文件中得到样本名 bcftools query -l input.vcf bcftools query -l input.vcf.gz bcftools query -l input.vcf > samples_name_list.txt bcftools query -l input.vcf.gz > samples_name_list.txt 查看vcf文件中的样本数量: bcftools query -l file.bcf | wc -l ...
使用bcftools query -l test.vcf > 453.list 将vcf文件中的样品名提取出来 不使用软件: head -100 all.vcf |grep "#C" |cut -f10-|xargs -n 1 > wild.txt 使用sh脚本 #将453份数据写入变量$sample for sample in $(cat 453.list); #创建每个样本的list文件 ...
ret = bcf_hdr_set_samples(args->hdr, args->query_sample.name, 0); tmp.s = args->query_sample.name; } if ( ret<0 ) error("Error parsing the list of samples: %s\n", tmp.s); else if ( ret>0 ) error("The sample not found in the VCF: %s\n", ret==1 ? args->qu...
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[i].setter ) // variable, query the VCF line filter->filters[i].setter(filter, line, &filter->filters[i]); else if ( filter->filters[i].key ) // string constant { filter->filters[i].str_value.l = 0; kputs(filter->filters[i].key, &filter->filters[i].str_value); filter-...
-l INT 设置压缩水平,0(未压缩)--9(最佳压缩) -@ INT 设置使用的线程数 例子 $ samtoolssorta.bam a.sort 3. merge 将2个或2个以上的已经sort的bam文件合并成一个bam文件,合并后的文件不需要再次sort,是已经sort过了的。 Usage:samtools merge [-nr] [-h inh.sam] <out.bam> <in1.bam> <in2....