-o FILE output file name [stdout] -R FILE list of read groups to be outputted [null] -f INT required flag, 0 for unset [0] -F INT filtering flag, 0 for unset [0] Skip alignments with bits present in INT [0] 数字4代表该序列没有比对到参考序列上 数字8代表该序列的mate序列没有比...
$ samtools view abc.sort.bam | less -S 1. 2. 3.merge 将2个或2个以上的已经sort了的bam文件融合成一个bam文件。融合后的文件不需要则是已经sort过了的。 Usage: samtools merge [-nr] [-h inh.sam] <out.bam> <in1.bam> <in2.bam>[...] Options: -n sort by read names -r attach RG...
As elsewhere in samtools, use '-' as the filename for stdin/stdout. The input file must be grouped by read name (e.g. sorted by name). Coordinated sorted input is not accepted. Example:samtools fixmate in.namesorted.sam out.bam reheader-- replace BAM header 替换bam文件头注释信息 $ s...
sort对bam文件进行排序。 Usage:samtools sort[option]<in.bam>-o<out.prefix>-nSortby read name#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排序。-mINTSetmaximum memory per thread;suffix K/M/Grecognized[768M]# 设置每个线程的最大内存,单位可...
sort sort alignment file split splits a file by read group quickcheck quickly check if SAM/BAM/CRAM file appears intact fastq converts a BAM to a FASTQ fasta converts a BAM to a FASTA collate $samtools collate Usage: samtools collate [-Ou] [-o <name>] [-n nFiles] [-l cLevel] <...
将2个或2个以上的已经sort了的bam文件融合成一个bam文件。融合后的文件不需要则是已经sort过了的。 Usage: samtools merge [-nr] [-h inh.sam] <out.bam> <in1.bam> <in2.bam>[...] Options: -n sort by read names -r attach RG tag (inferred from file names) -u uncompressed BAM output ...
-o FILE output file name [stdout] -R FILE list of read groups to be outputted [null] -f INT required flag, 0 for unset [0] -F INT filtering flag, 0 for unset [0] Skip alignments with bits present in INT [0] 数字4代表该序列没有比对到参考序列上 ...
longer help ./samtools sort usage: samtools sort options options: -n sort by read name -f use as full file name instead of prefix -o final 7、 output to stdout -l int compression level, from 0 to 9 -1 - int number of sorting and compression threads 1 -m int max memory per ...
将2个或2个以上的已经sort了的bam文件融合成一个bam文件。融合后的文件不需要则是已经sort过了的。 Usage: samtools merge [-nr] [-h inh.sam] <out.bam> <in1.bam> <in2.bam>[...] Options: -n sort by read names -r attach RG tag (inferred from file names) ...
samtools sort [-l level] [-m maxMem] [-o out.bam] [-O format] [-n] [-t tag] [-T tmpprefix] [-@ threads] [in.sam|in.bam|in.cram] -m 设置内存使用大小,默认是500,000,000(现在支持K,M,G等缩写) -n Sort by read names (i.e., the QNAME field) rather than by chromosomal...