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...
Input g.vcf or g.vcf.gz 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 ...
vcf格式 Variant Call Format(VCF)是一个用于存储基因序列突变信息的文本格式.表示单碱基突变, 插入/缺失, 拷贝数变异和结构变异等.BCF格式文件是VCF格式的二进制文件. CHROM [chromosome]: 染色体名称. POS [position]: 参考基因组突变碱基位置,如果是INDEL(插入缺失),位置是INDEL的第一个碱基位置. ID [identifier...
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-dir is not specified. (default: None) -...
appropriate service role. This role must be able to read from any Amazon S3 location where your data resides. If you are using a customer managed key(CM-CMK), you must also use the AWS KMS decrypt permissions. It must also have the appropriate trust policy for HealthOmics to assume the ...
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...
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 ...
你这个不是GVCF,不能用这个方法合并;
_add_acgt_depths_to_minos(minos_records, acgt_depths) else: acgt_depths = {} ref_seqs = {} pyfastaq.tasks.file_to_dict(ref_fasta, ref_seqs) used_ref_seqs = set() ref_seq = None ref_pos = -1 minos_record = None logging.info(f"Making GVCF file {out_vcf} from {minos_vcf}...
java -Djava.io.tmpdir=/path/to/tmpdir 但是现在就是进退两难了,因为加上这个参数,命令提交到服务器就被kill,如果不加上这个参数,我们的临时目录又没有空间让我运行这个gatk命令。 首先需要简单了解一些java java -version:查看JDK版本 whereis java