-R human.fasta \ --emitRefConfidence GVCF \ -L chr1 \ #染色体名称 -I sample_name.realigned.bam \ -o sample_name.split.bam.chr1.gvcf \ #每个染色体对应的gvcf文件 就只增加了一个 -L 参数,通过这个参数我们可以指定特定的染色体(或者基因组区域)!我们这里指定的是 1 号染色体,有些地方会写成ch...
你这个不是GVCF,不能用这个方法合并;
Panel variant overlaps a reference block. Every panel variant within a reference block will have a homozygous reference genotype and the same PL based on the catch-all <NON_REF> ALT. Panel variant matches a sample variant. Two variants are defined as matching if and only if: ...
if ref_seq is not None: # happens if the samtools VCF was empty _finish_contig(ref_pos, ref_seq, minos_record, minos_iter, f_out) _print_non_samtools_seqs(ref_seqs, used_ref_seqs, minos_records, f_out) 6 changes: 5 additions & 1 deletion 6 python/clockwork/tasks/gvcf_from_minos...
Contiguous non-variant segments of the genome can be represented as single records in gVCF. These records use the standard 'END' INFO key to indicate the extent of the record. Even though the record can span multiple bases, only the first base is provided in the REF field to reduce file ...