I have been struggling with running samtools because the program can not read the header of my sam file so i get the following error: samtools sort: failed to read header from "20201032.sam" samtools sort: failed to read header from "20201032.sam" samtools sort: failed to read header fr...
Processing 2503 unmapped reads. The first unmapped read has length 79. Low quality read marking (-s lowq)... --> Skipped low quality read marking. rDNA profiling (-s rdna)... samtools sort: failed to read header from "-" The logfile example--02_rdna.log says the following: (ERR):...
samtools sort: failed to read header from "file_sorted_fixmate.bam" + samtools markdup file_sorted_fixmate_position.bam Usage: samtools markdup <input.bam> <output.bam> Option: -r Remove duplicate reads -l INT Max read length (default 300 bases) -S Mark supplementary alignments of duplicate...
如果你记住了 RTFM ，你还会通过 samtools sort 那行前面的 -T 知道后面是什么东西[2]<scratchPath> ...
-h FILE copy the header in FILE to <out.bam> [in1.bam]。 指定FILE内的’@’头复制到输出bam文件中并替换输出文件的文件头。否则,输出文件的文件头将从第一个输入文件复制过来; -n sort by read names。设定输入比对文件是以read名进行排序的而不是以染色体坐标排序的; -R STR merge file in the ...
Options: -n sort by read names -r attach RG tag (inferred from file names) -u uncompressed BAM output -f overwrite the output BAM if exist -1 compress level 1 -R STR merge file in the specified region STR [all] -h FILE copy the header in FILE to <out.bam> [in1.bam] 例子: ...
samtools sort Usage: samtools sort [options...] [in.bam] Options: -l INT Set compression level, from 0 (uncompressed) to 9 (best) -m INT Set maximum memory per thread; suffix K/M/G recognized [768M] -n Sort by read name -t TAG Sort by value of TAG. Uses position as secondary...
Options: -n sort by read names -r attach RG tag (inferred from file names) -u uncompressed BAM output -f overwrite the output BAM if exist -1 compress level 1 -R STR merge file in the specified region STR [all] -h FILE copy the header in FILE to <out.bam> [in1.bam] ...
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 -- Statistics bedcov read depth per BED region ...
# 根据fasta文件,将 header 加入到 sam 或 bam 文件中 samtools view-Tgenome.fasta-h scaffold1.sam>scaffold1.h.sam 具体例子: 2.samtools sort 代码语言:javascript 代码运行次数:0 复制 Cloud Studio代码运行 samtools sort用来对SAM/BAM/CRAM文件进行排序,按最左坐标排序,或使用-n时按读取名称排序。默认情...