[E::sam_index] Read '***' with ref_name='hic_scaffold_1', ref_length=569202264, flags=97, pos=536870753 cannot be indexed samtools index: failed to create index for "***.bam": Numerical result out of range 通过检测samtools版本发现 samtools --version 检测版本 进而通过查阅发现其他策略解...
Thesamtools indexcommand can now accept multiple alignment filenames with the new-Moption, and will index each of them separately. (Specifying the output index filename via out.index or the new-ooption is currently only applicable when there is only one alignment file to be indexed.) (PR#...
As my bam file can not be open by ANGSD, I did some exploration in samtools, what I found: santools view XXX.bam | head works. samtools index XXX.bam, didn't work, the error is: [E::hts_idx_push] Region 1747042382..1747042497 cannot be stored in a bai index. Try using a csi...
[E::hts_idx_check_range] Region 536870922..536871063 cannot be storedina bai index. Try using a csi index[E::sam_index] Read'E00548:269:HV7NVCCXY:3:2117:26494:57301'with ref_name='chr1H', ref_length=558535432, flags=81, pos=536870923 cannot be indexed samtools index: failed to cr...
[E::hts_idx_check_range] Region 536870922..536871063 cannot be stored in a bai index. Try using a csi index[E::sam_index] Read 'E00548:269:HV7NVCCXY:3:2117:26494:57301' with ref_name='chr1H', ref_length=558535432, flags=81, pos=536870923 cannot be indexed ...
Index reference sequence in the FASTA format or extract subsequence from indexed reference sequence. If no region is specified, faidx will index the file and create <ref.fasta>.fai on the disk. If regions are specified, the subsequences will be retrieved and printed to stdout in the FASTA for...
thrownewSAMException("BAM cannot be indexed without setting a fileSource for record "+rec); } finalChunknewChunk=((BAMFileSpan)rec.getFileSource().getFilePointer()).getSingleChunk(); finallongstart=newChunk.getChunkStart(); finallongend=newChunk.getChunkEnd(); ...
Linux的管道命令 管道命令(Pipe) 管道命令用"|"来表示,管道命令需要接收前一个命令的输出来进行操作,但...
index 为sort后的bam文件建立所以,这是在 view 比对结果时指定染色体区域必须做的。 samtools index aln.sorted.bam rmdup 去除可能的PCR重复。将比对到相同位置的reads去重,仅保留比对质量最好的一个。一般只对paired end reads(fr)有效,并须指定ISIZE。
samtools faidx <ref.fasta> [region1 [...]] fixmate Index reference sequence in the FASTA format or extract subsequence from indexed reference sequence. If no region is specified, faidx will index the file and create <ref.fasta>.fai on the disk. If regions are speficified, the ...