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...
sort命令还会在内存不足时创建临时文件tmpprefix.%d.bam Options: -m 设置每个线程运行时的内存大小,可以使用K,M和G表示内存大小。默认下是 500,000,000 即500M。对于处理大数据时,如果内存够用,则设置大点的值,以节约时间。 -n 设置按照read名称进行排序。默认下是按序列在fasta文件中的顺序(即header)和序列从...
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] 例子: ...
FAILED: 0 WRITTEN: 6352529 格式转换 -- File operations collate shuffle and group alignments by name cat concatenate BAMs merge merge sorted alignments mpileup multi-way pileup sort sort alignment file split splits a file by read group quickcheck quickly check if SAM/BAM/CRAM file appears intact...
samtools的sort功能可以将基因组比对文件中的每一条read按照染色体标号（或者是contig标号）以及位置升序排列...
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 ...
Usage:samtools merge[-nurlf][-h inh.sam][-b<bamlist.fofn>]<out.bam><in1.bam>[<in2.bam>...<inN.bam>]Options:-n Input files are sorted by read name # 输入文件是经过sort-n的-tTAGInput files are sorted byTAGvalue # 输入文件是经过sort-t的-r AttachRGtag(inferred from file names...