首先,这两者都是 VCF 文件,都由HEADER和RECORDS组成。 不同之处在于GVCF文件会记录更多的信息,这里更多的信息是指未突变的位点的覆盖情况。从下面的图我们可以直观地看出两者的区别: 可以看到,GVCF文件也分两种,一种是-erc gvcf ,另一种是 -erc bp_resolution,这两种gvcf文件的区别在于前一种GVCF文件记录非突变...
genotypegvcf Reference Convert GVCF to VCF. Input/Output file options --ref REF Path to the reference file. (default: None) Option is required. --in-gvcf IN_GVCF Input a g.vcf or g.vcf.gz file that will be converted to VCF. Required if--in-selectvariants-diris not specified. (defaul...
老师我重新下载了镜像，在生成.g.vcf.gz文件时还是没有内容只有表头。报错如下A USER ERROR has occurr...
Input g.vcf file that will be converted to VCF. Required if--in-selectvariants-diris not specified. --in-selectvariants-dir Path to the output directory of selectvariants. Required if –in-gvcf is not specified. --out-vcf (required)Output VCF file. ...
工具来构建索引。gatk --java-options "-Xmx50g" IndexFeatureFile -I **.g.vcf.gz ...
This tool provides basic genome VCF (GVCF) merging and genotyping functionality to provide a multisample BCF/VCF suitable for cohort analysis. Variants are normalised and decomposed on-the-fly before merging. Samples that do not have a particular variant have their homozygous reference confidence esti...
cyvcf2 (managed via conda) gatk4 (managed via conda) Building Install conda clone this github repository (recursively to get the correct GLIMPSE version)git clone https://github.com/mctp/lopass --recursive Executebuild.shscript, this will compileGLIMPSE ...
-ERC GVCF -L $bed -R $GENOME -I $bam --dbsnp $DBSNP -O ${sample}_raw.vcf fi i=$((i+1)) done 最后把多个gvcf文件合并 因为合并只能一次给定一个区间,所以需要分染色体来做,正好相当于是并行!!! 代码语言:javascript 复制 forbedinchr{1..22}chrX chrYdoif((i%$1==$2))then ...
but the next PL isPL(1/1) = 26(which corresponds to 10^(-2.6), or 0.0025). QUAL和GQ的区别: GVCF和VCF的最大区别是在于GVCF文件会记录所有的点,包括哪些没有突变的点。 在GVCF模式下,那些没有变异的点会形成一个未变异块,non-var block record。
but the next PL isPL(1/1) = 26(which corresponds to 10^(-2.6), or 0.0025). QUAL和GQ的区别: GVCF和VCF的最大区别是在于GVCF文件会记录所有的点,包括哪些没有突变的点。 在GVCF模式下,那些没有变异的点会形成一个未变异块,non-var block record。