Bam no header bam; BTW, the problem was the /n@/ part of your command. sam # extract header only samtools reheader header. bam": No such file or directory INFO 2021-06-09 12:35:59,164 done making mutations, merging mutations into BM. bam --HD "@hd VN:1. Sign in Product When i looked the same file with head command i could see the first 10 header lines. See below for details: shell: "minimap2 -a -k 19 -w 10 -I 10G -g 5000 -r 2000 --lj-min-ratio 0. bam x. It is fine for me. And now its reading the sam file. Everything seems okay until I run the command to call ChrM region. You are probably aligning against a "multi-part" index. The error message could be more That's exactly the problem: The -U option is to Output reads not selected by filters to FILE, but the option you want is the -u to get Uncompressed BAM output, which already samtools reheader – replaces the header in the input file SYNOPSIS. It might even be possible to pipe the first command to the second, but I haven't tested that Comment. Copy link Gimenagomez2230 commented Oct 26, 2023. Although it don't complete now, I can read the head of generated sam file by samtools view. Hi, guys! I'm a complete noobie in computational staff and just trying to learn thing. bam chrM > chrM. Each of those contigs will have an @SQ line in the header. jar and ReplaceSamHeader. However, I get the following error: [E::bam_hdr_write] Header too long for BAM format [main_samview] failed to write the SAM header header内容不多，也不会太复杂，每一行都用‘@’ 符号开头，里面主要包含了版本信息，序列比对的参考序列信息，如果是标准工具（bwa，bowtie，picard）生成的BAM，一般还会包含生成该份文件的参数信息（如上图），@PG标签开头的那些这里需要重点提一下的是header中的@RG也就是Read group信息，这是在做 The fasta header has two spaces and the descriptions are identical except the second description has a bit more information. 尝试改变参数也不行就查看了sam文件#head -10 ra24p. The conversion requires 2 hours per . The input is probably truncated. fai -o aln. txt and perhaps remove the "--" from all your header lines, then use "samtools reheader" with your new header file and the bam file. As the downstream programs further process the alignments, The input is probably truncated. Hello, I installed and ran SimSeq according to the README file and then I tried to view the created out. bam with the header in in. 3. 0 SO:unknown @HD VN:1. I think the problem is that your awk statement is resulting in a . sam >SRR3589956. bam where ref. sorted. 1-217-g6 Tools (written in C using htslib) for manipulating next-generation sequencing data - samtools/bam_reheader. pl). This results in no SQ headers in the bam file. The Illumina sequencing machine generated a BAM file with no table of reference names and lengths, and no @SQ lines, as it did not have that information. [samopen] no @SQ lines in the header. Basically use "samtools view -H file. Im now trying to use samtools markdup to remove the duplicate/over-represented sequences and IS THERE A TOOL THAT WILL CHECK THAT A BAM HEADER IS VALID? headers BAM • 1. Sam/Bam Manipulation. bam > new. 3 SO:coordinate"I ran class:inverse middle center # Getting to know BAM files ---- <br> <br> <br> ### Jelmer Poelstra, MCIC Wooster ### 2021/03/05 (updated: 2021-03-04) --- ## Recap for No problem! It's hard to know exactly what to expect to see in your header without knowing the entire workflow, but it looks like you aligned against reference with many contigs. Entering edit mode. bam --out file_with_header. -t FILE A tab-delimited FILE. with samtools view -b -T ref. sam[M::bwa_idx_load__sam to bam As you can see there is no @HD header in the first line. fa samtools view -bt ref. bam with the header If I use this command, > $ samtools view -h unsorted. The . samtools view generates one, it just keeps the one that should already be there. bam with the same content and sorting as the input file, except the SAM record header's @RG line will be updated with the new information for the specified fields and each read will now have I would like to convert a large sam file created by bowtie2 to bam (and subsequently sort/index downstream process): samtools view file. png 这样才可以正常运行 [bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files Usage: samtools sort [options] [in. you are probably better off with addreplacerg [E::bam_hdr_write] Header too long for BAM format samtools merge: failed to write header to "addsnv. bam | head showed me this and don't know what means the @hd VN:1. pdf which is not a The only "append" function is bam_aux_append. bam note that the unsorted. Each line must contain the reference name in the first column and the length of the reference in the second column, with one line for each distinct reference. clean. [main_samview] fail to read the header from "/workspace/home/goat/wangzq In commit b363b23 I added the option to avoid checking the BAM headers -checkBamBeaders 0. 在这一步中使用的测序结果数据RNA. bam > Here is how a BAM format starts: magic BAM magic string char[4] l_text Length of the header text, including any NUL padding int32 text Plain header text in SAM; not necessarily NUL-terminated char now edit the l_text and text while shifting the file as needed. This causes issues with ANGSD:-> Inputtype is BAM/CRAM -> We require a proper header starting with @HD for ANGSD -> We observed: '@SQ SN:sca' will exit How can I get bwa mem to output the @HD file? I'd prefer this than having to add it manually. Illumina is using a BAM file in this instance for unaligned, raw data. bam aln. 使用-h参数将header引入才可以转换回sam文件以供手动检查。 I agree, the method worked fine for me, but I had to redirect the output of the samtools/reheader command to a newly created bam file, otherwise the file with the correct header is printed to the screen and then the remote terminal crashed: samtools reheader header_corrected. Seegmentation fault (core dumped) The problem seems to be in the SAM-->BAM conversion My SAM file seems OK (obtained with the Illumina script : illumina_export2sam. fq > aln. sam" instead of "samtools view -hSbo x. sam > ra24p. If I use this command, > $ samtools view -h unsorted. Import SAM to BAM when @SQ lines are present in the header: samtools view -bo aln. If the need arises, Samtools can also be used to modify the header of a . sam -o out. Methods used in this tutorial include: minimap2 - to create alignments of a long-read sequencing dataset, samtools - to inspect and filter SAM and BAM files, and 具体报错内容为 [bam_header_read] invalid BAM binary header (this is not a BAM file). It wasn't produced at least by v2. fai is generated automatically by the faidx command. [main_samview] fail to read the header from "test. fastq. Examples. bam but it still has no header. bam Traceback (most recent call last): File "/opt/cesga/easybuild This creates a file called reads_addRG. Post Cancel. Or one may be created/edited for use with writing to a new file (via BamWriter). The BamHeader class represents the header section of the BAM file. . sam The tag [ID] required for [PG] not present. bam BX. 1k次。这篇博客介绍了如何利用samtools工具快速生成hg38参考基因组的FAI索引，并从SAM文件转换成BAM文件，解决了转换过程中遇到的问题。通过 samtools view 命令，将chr5的配对读取 SAM 文件转换为 BAM 文件，简化了工作流程。 Introduction to SAM and BAM files. Does anyone have any suggestions as to how to deal with this? Considering that only a single one of the BAM files is missing a header, I'm hoping there is some way to repair it, using the same header found in all the other BAM files. Edit header. You can't create a BAM file without a header. header. A BamHeader may be fetched from a BamFile to view an existing file’s metadata. bam[samopen] no @SQ lines in the header. bam If @SQ lines are absent: samtools faidx ref. I had a small number of RG tags in each BAM file. -i, --in-place Perform the header edit in-place, if possible. The input alignment file may be in SAM, BAM, or CRAM format; if no FILE is specified, standard input will be read. You can probably half-ass it by just getting a sorted list of chromosomes from your SAM file: samtools head – view SAM/BAM/CRAM file headers SYNOPSIS samtools head [-h INT] [-n INT] [FILE] DESCRIPTION By default, prints all headers from the specified input file to standard output in SAM format. Thanks!! Shall convert to bam file now. jmarshall. The command for calling ChrM that I have used but my BAM file doesn't have a header: samtools view DMSO. muts. sam > aln. If you are working with high-throughput sequencing data, at some point you will Until now, I cannot figure out to add the RG to the bam file as the RG header is absent in the files. b0ed8228-36ee-43d0-8cde-8e1a5a48fc15. If @SQ lines are absent: samtools faidx ref. STAR output Bam has no header #1979. 一、sam、bam简介 1、sam Sequence Alignment/Map format，直译就是序列比对格 小贝学生信 阅读 5,993 评论 0 赞 11 sam文件转换为bam文件——SAMtools Replace the header in in. hi all, reading the bam file using the code below samtools view -H 388. ran-fq2bam does not add the sample name to the readgroups by default, so although the seperate GVCF are produced, they lack sample IDs. Do not add a @PG line to the header of the output file. sam" (or something like that). I created the reference. [sam_read1] missing header? Abort! There's no need to make a SAM file (step 2), especially since you're not using it. g. bam the -h can include the header in the With no options or regions specified, prints all alignments in the specified input alignment file (in SAM, BAM, or CRAM format) to standard output in SAM format (with no header). info) The best (and likely fastest) solution would be to use the minimap2-I option and give minimap lots of memory, as suggested in the FAQ. volks. fai unsorted. My questions: Given a bam_hdr_t header (potentially empty), how to add a new chromosome reference? (For example, add a new chrAB to the BAM file) Given a non-empty bam_hdr_t * header, how to remove a chromosome? (For example, remove chr4 from the BAM header) My 使用samtools的-b参数完成sam->bam格式转换（sam：纯文本，可读性好；bam：二进制文件，后续处理效率更高） $ samtools view -b celegans. Usage. It provides metadata about the file including file version, reference sequences, read groups, comments, etc. To reproduce, run the following commands on this file: TM433_trunc. > > > Could you please do me To display only the headers of a SAM/BAM/CRAM or VCF/BCF file, use head: Both head commands also have options to limit the number of header lines displayed and/or to display The command was: samtools view -h file. sam > celegans_copy. fai with The BAM/SAM handling functionality in to-mr is directly taken from the samtools package, as you can see from the source codes. 文章浏览阅读9. bam #重定向符也可以换成-o参数 samtools view -h SRR3589956. For MuTect2, your bam files need to have sample names in the SM field in the header that starts with the @RG, and then passed the sample names onto --normal-sample and --tumor-sample arguments. The open file function always looks for a header no matter the input format. 经过了第四节的长文，我想大家基本上已经知道了一个wgs流程该如何构建起来了吧。但在那一节中限于篇幅有两个很重要的文件我没能展开来讲，分别是：bam和vcf文件。 The header is usually multiple lines and has information no chromosomes and samples included in the . The samtools quickcheck does not find this malformation. STARAligned. But that's for optional fields. Reload to refresh your session. samtools reheader [-iP] in. Picard软件的AddOrReplaceReadGroups方法； 两种方法有什么区别呢？Samtools仅能修改header信息，但是picard不仅能修改header信息，还可以用户自定义添加read group信息。所以如果你没有什么高级的需求用samtools就可以（因为速度更快）。 本篇是自己学习SAM和SAMtag的资料心得，详细介绍高通量测序中SAM/ BAM 格式文件。 本文将了解什么？ 欢迎微信搜索关注@pythonic生物人 1、SAM/BAM格式简介 2、术语与概念理解 3、标头部分（header section）详述 4、比对信 Is there any other way to determine for a BAM file what human reference genome was used for alignment if this info is not able to be ascertained from the header of the BAM file? (We have come across some human BAM files where the header does not contain enough info to determine the reference genome used for alignment. ok. unique. In this case, minimap2 is unable to output a proper header. The GATK no longer supports SAM files without read groups I have tried Picards AddOrReplaceReadGroups. Thanks Colin With no options or regions specified, prints all alignments in the specified input alignment file (in SAM, BAM, or CRAM format) to standard output in SAM format (with no header). Continue anyway. samtools reheader [-iP] [-c CMD | in. I don't think you can create a legit BAM file without a header, though. Gimenagomez2230 opened this issue Oct 26, 2023 · 1 comment Comments. sam -o unsorted. bam No validity checking is performed on the header, nor that it is suitable to use with the sequence data itself. 3 seems to work quite well. sam with no header, and I don't think . Navigation Menu Toggle navigation. Then I manually wrote the header files and added the new header to the existing bam file using the samtools reheader tool. sam > out. fa in. sam has no header @SQ then I tried this, $ samtools view -hbt hg19. samtools quickcheck does not SEARCH this Replace the header in in. bam > (unsorted. Although another possibility would be to make your own header using samtools dict and then Replace the header in in. 2k views ADD COMMENT • link 2. 5. jar but it didn't help me. sample_name. This only works on CRAM files and only if there is Older versions of samtools would happily merge BAM files with no @HD header line, new versions on the develop branch fail: $ . You switched accounts on another tab or window. sam] in. However with the above command its showed as failed to read. I checked the newly generated SAM file with header @PG. ) Hello, 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 index: failed to open "20201032_sorted. When you use BWA to align reads, you need to pass on the header like -R '@RG\tID:MY_ID\tLB:MY_LIBRARY\tPL:illumina\tSM:Tumor_Sample_Name'. fa to use. out. 文件中的header行SAM文件中的header以 @开头 You signed in with another tab or window. I get the new. Could this be the problem? None of the upstream used tools had a problem with the header and other samtools commands also do not seem to mind it With the latest version (see PR #94) I get a AttributeError: 'str' object has no attribute 'items' if the bam file that contains a @CO header line. When I tried to use command line, like" samtools view -b in. I have rerun the alignment once again. Just use samtools view -b sorted. To make sure the header is correctly written, I validated the file again. sam [bam_header_read] EOF marker is absent. withamperrors. SAMtools provides various (sub)tools for manipulating alignments in the SAM/BAM format. I have encountered an issue when using rna_fq2bam followed by haplotypecaller and then gatk combineGVCFs. Binary Alignment Map (BAM) is the comprehensive raw data of genome sequencing; [1] it consists of the lossless, compressed binary representation of the Sequence Alignment Map-files. fa. bam". bam. We can ask the view command to report solely the header by using the -H option. sam header. But yeah, giving the variant caller a BED file is the simplest solution overall and allows you to skip subsetting the BAM file as well. sam. sam file. The SNP caller isn't going to call variants where there are no alignments. c at develop · samtools/samtools [bam_header_read] invalid BAM binary header (this is not a BAM file). 是在上一步生成sam文件时出现问题。 命令： minimap2 -ax map-ont RNAseq. Samtools can be used to view the header of a . 介绍两种更改bam文件header的方法： 1. "So I did: samtools reheader old. View 作用：bam与sam互转，查看bam文件，对bam进行排序和提取的操作。 -sam与bam互转:-S指定输入文件格式为sam，不加则为bam,-b指定输出格式(默认输出sam) samtools view -Sb SRR3589956. 2-216-gdffc67f Using htslib 1. bam is the output of sam -> bam conversion) > Then I can see the header in unsorted. SAMTools quickcheck gives the following error: had no targets in header. Comment. So, when it gets to the joint calling step the combined VCF files only contains one sample as there were no Is there any other way to determine for a BAM file what human reference genome was used for alignment if this info is not able to be ascertained from the header of the BAM file? (We have come across some human BAM files where the header does not contain enough info to determine the reference genome used for alignment. /samtools --version samtools 1. DESCRIPTION. This command is much faster than replacing the header with a BAM→SAM→BAM conversion. The program also now prints out the offending headers so users can see which BAMS are problematic. Header—The sample name, sample length, and alignment method are all included in this section. 5 years ago by sbilobram &utrif; 20 0. ) With no options or regions specified, this command prints all alignments in the specified input alignment file (in SAM, BAM, or CRAM format) to standard output in SAM format (with no header). You may specify one or more space-separated region specifications after the input filename to restrict output to only those alignments which overlap the specified region(s). 5 " "-A 2 -B 5 -O 5,56 -E 4,1 -z 400,50 --sam-hit-only -t {threads [bam_header_read] invalid BAM binary header (this is not a BAM file). $ samtools view -bt hg19. In The problem is you have mapped reads in your file, but no @SQ line in the header to indicate where those reads are mapped to (a reference). However, i don't know which ref. o Import SAM to BAM when @SQ lines are present in the header: samtools view -bS aln. sam old. bam | head -n 5 Aha, I see the problem. Replace the header in in. sam in. bam is malformed: SAM file doesn't have any read groups defined in the header. bam > file. bad. Here is the first line of sam, I guess there is still no header: Without knowing the chromosome names and sizes, you won't be able to make a BAM file (there'd be no way for it to know how to create the header). Then for ##### ERROR MESSAGE: SAM/BAM file /path/my_reordered. It could be possible if the index were created on (BX, POS) rather than the typical (RNAME, POS). txt". This command will give you a warning that no @SQ lines are present but will generate an output BAM. You have to manually add it (e. bam " to generate BAM file, it occurs errors: [bam_header_read] EOF marker is absent. fai aln. The output from your program was 'Problem with number of chromosomes in header', so maybe you looked at the wrong BAM headers? The program 理解并操作bam文件. In fact, nobody has that information, it's unknown. The input is probably t The way I ended up fixing this was by installing BamUtil, which has PolishBam where you can run the command: bam polishbam --in file_no_header. All references used before had only one description -> one space. sam file also has no header when I @jkbonfield A bit off topic, but I do have occasion where I'd like to index a barcode-sorted BAM file, so that I can extract all the alignment of a particular barcode using samtools view foo. bam" at the beginning of the command). Some of the BAM files that are created during sorting and duplicate removal are not readable with samtools view, and generate errors like: samtools view BGL-112-003_ATCACG_R2. gz是fasta格式的，错误。 Hi, because Megalodon produces rather odd (but v useful!) bam files, it might make sense to add the PG tag to the bam header if possible. Samtools工具的reheader方法； 2. The headers in Dorado base called (simple and duplex) as well as alignmnent bam files are incomplete. I want to convert SAM file to BAM and my SAM file does not have a header. But if I open the file (using the -u option in the last pipe to avoid compression), I see Learning the BAM format Introduction. gz. You can add --split-prefix=pre to the MinimapToBam rule in the snakemake file and it should then work properly. Samtools uses the reheader command to do this. I used the ValidateSamFile tool from Picard to get the different RG tags in the alignment section. More simply, since the BAM file was already subset, simply doing nothing would suffice. I'm guessing that's the majority of I have the following problem: my sam file contain no headers, so I can't convert it to bam directly, I get the following error: > samtools view -S accepted_hits. fa sample_name. Did you create the BAM file without a header? Presumably you did a "samtools view -Sbo x. -H print header only (no alignments)-S input is SAM-u uncompressed BAM output (force -b)-x output FLAG in HEX It's likely the problem is due to trying to create a BAM file from input with no header (try a "samtools view -h acc_hits. The tutorial is intended as a gentle introduction to Sequence Alignment/Map (SAM) formatted files and their binary equivalents BAM. 0 SO:unknown @SQ SN:1 LN:248956422 Skip to content. min RNA. bam [bam_header_read] bgzf_check_EOF: Invalid argument [bam_header_read] invalid BAM binary header (this is not a BAM file). The SAM (Sequence Alignment/Map) format (BAM is just the binary form of SAM) is currently the de facto standard for storing large nucleotide sequence alignments. Had you used /^@/ then you would have been fine, though that's still much slower than what I showed above. bam > header. Manual-P, --no-PG Do not generate an @PG header line. This conflicts with this 'mandatory' table. --no-PG. Samtools samtools 1. Join Date: Jun 2010; Posts: 80; As you can see there is no @HD header in the first line. So, I goggle the problem and found one possible solution with -t options from samtools. samtools view -H file. 2. gz >RNA. cram seems to be 10 times smaller than the corresponding . There is in fact a tool bxtools convert for this purpose, that . As regards to the re-conversion cram -> 文章浏览阅读2. bam": No such file or directory srun: error: Still don't get headers. bam file. toTranscriptome. bam) as a post step. [bam_header_read] bgzf_check_EOF: Invalid argument [bam_header_read] invalid BAM binary header (this is not a BAM file). sam using samtools: [khaleel@alanine examples]$ samtools view out. The modified command is minimap2 -t 30 -2 -I 100g -ax map-pb genome. A USER ERROR has occurred: Bad input: Sample sample20170711-4_I6_S6_L007 is not in BAM header: [Msample20190927-1-I44_L4_D95T59, sample20170711-4_I6_S6_L007_R1] image. By default this command outputs the BAM or CRAM file to standard output (stdout), but for CRAM format files it has the option to perform an in-place edit, both reading and writing to the same file. sam -o file. bam] Options: -l INT Set compression level, from 0 (uncompressed) to 9 (best) -u Output uncompressed data (equivalent to -l 0) -m INT Set maximum memory per thread; suffix K/M/G recognized [768M] -M Use minimiser for clustering class PacBio::BAM::BamHeader¶. [bam_sort_core] truncated file. > > > Could you please do me a favor to take a look at the problem as follows? Let’s also inspect just the header. [bam_header_read] invalid BAM binary header (this is not a BAM file). You signed out in another tab or window. Member. Without the @SQ information all of your alignment entries will have no chromosome name (just '*') and all of the positions will be '0'. The resulting BAM will be worthless though. Closed Gimenagomez2230 opened this issue Oct 26, 2023 · 1 comment Closed STAR output Bam has no header #1979. 6k次，点赞2次，收藏4次。开始学习生物信息分析，在ubuntu上运行了samtools view，结果显示错误，如下：# samtools view -@ 60 -bS *. The header in a bam file records important information regarding the reference genome to which the reads were aligned, as well as other information about how the BAM has been processed. SAM|BAM 文件格式解析 程序标准输出文件，以TAB作为分隔符，并且前几行通常是一些header（可选）。 1. where ref. bam file with the following command. BAM文件中除了必须的前11列信息之外，不同的BAM文件中后面记录metadata的列是不固定的，在不同的处理软件中输出时也会有所不同，meatdata含义：SAM (Sequence Alignment/Map) Format Alignment Tags (samformat. bam --> BM. nqrxe emrprm nnasso ybksb wcnor jngvh ehdd gcp yahqb bsmbnu pwvb ofpjnby nyzndbq nggkv nml