Bam no header. 5 years ago by sbilobram ▴ 20 0.

Bam no header bam [bam_header_read] bgzf_check_EOF: Invalid argument [bam_header_read] invalid BAM binary header (this is not a BAM file). pl). with samtools view -b -T ref. sam > ra24p. 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. header. Manual-P, --no-PG Do not generate an @PG header line. gz >RNA. sam] in. bam x. STARAligned. ) 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). withamperrors. bam[samopen] no @SQ lines in the header. pdf which is not a The only "append" function is bam_aux_append. 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). The . toTranscriptome. 3. Samtools uses the reheader command to do this. Closed Gimenagomez2230 opened this issue Oct 26, 2023 · 1 comment Closed STAR output Bam has no header #1979. 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. 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. 尝试改变参数也不行就查看了sam文件#head -10 ra24p. . sam[M::bwa_idx_load__sam to bam As you can see there is no @HD header in the first line. 0 SO:unknown @SQ SN:1 LN:248956422 Skip to content. sorted. When I tried to use command line, like" samtools view -b in. /samtools --version samtools 1. 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 . sam in. Thanks!! Shall convert to bam file now. fai aln. 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. STAR output Bam has no header #1979. See below for details: shell: "minimap2 -a -k 19 -w 10 -I 10G -g 5000 -r 2000 --lj-min-ratio 0. bam BX. In this case, minimap2 is unable to output a proper header. Post Cancel. samtools view generates one, it just keeps the one that should already be there. where ref. samtools quickcheck does not SEARCH this Replace the header in in. bam --> BM. In fact, nobody has that information, it's unknown. ok. 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. bam". sam" instead of "samtools view -hSbo x. jar but it didn't help me. bam chrM > chrM. 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. out. If @SQ lines are absent: samtools faidx ref. Replace the header in in. bam No validity checking is performed on the header, nor that it is suitable to use with the sequence data itself. 介绍两种更改bam文件header的方法： 1. bam --out file_with_header. I have encountered an issue when using rna_fq2bam followed by haplotypecaller and then gatk combineGVCFs. ran-fq2bam does not add the sample name to the readgroups by default, so although the seperate GVCF are produced, they lack sample IDs. bam file. hi all, reading the bam file using the code below samtools view -H 388. fai unsorted. -i, --in-place Perform the header edit in-place, if possible. You are probably aligning against a "multi-part" index. o Import SAM to BAM when @SQ lines are present in the header: samtools view -bS aln. 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. sam old. bad. fa samtools view -bt ref. Header—The sample name, sample length, and alignment method are all included in this section. [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. 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). Edit header. So, I goggle the problem and found one possible solution with -t options from samtools. 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). > > > Could you please do me a favor to take a look at the problem as follows? Let’s also inspect just the header. Hi, guys! I'm a complete noobie in computational staff and just trying to learn thing. 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. fa sample_name. But that's for optional fields. The GATK no longer supports SAM files without read groups I have tried Picards AddOrReplaceReadGroups. 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. As regards to the re-conversion cram -> 文章浏览阅读2. bam; BTW, the problem was the /n@/ part of your command. 是在上一步生成sam文件时出现问题。 命令： minimap2 -ax map-ont RNAseq. 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. Had you used /^@/ then you would have been fine, though that's still much slower than what I showed above. The input is probably truncated. 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. I don't think you can create a legit BAM file without a header, though. Each of those contigs will have an @SQ line in the header. fastq. The tutorial is intended as a gentle introduction to Sequence Alignment/Map (SAM) formatted files and their binary equivalents BAM. Everything seems okay until I run the command to call ChrM region. The open file function always looks for a header no matter the input format. I think the problem is that your awk statement is resulting in a . sam The tag [ID] required for [PG] not present. And now its reading the sam file. The SNP caller isn't going to call variants where there are no alignments. I want to convert SAM file to BAM and my SAM file does not have a header. sam > celegans_copy. However with the above command its showed as failed to read. 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. 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. Hello, I installed and ran SimSeq according to the README file and then I tried to view the created out. bam but it still has no header. 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. Samtools can be used to view the header of a . I used the ValidateSamFile tool from Picard to get the different RG tags in the alignment section. 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. Gimenagomez2230 opened this issue Oct 26, 2023 · 1 comment Comments. 5 years ago by sbilobram &utrif; 20 0. Examples. sam has no header @SQ then I tried this, $ samtools view -hbt hg19. I checked the newly generated SAM file with header @PG. [bam_header_read] bgzf_check_EOF: Invalid argument [bam_header_read] invalid BAM binary header (this is not a BAM file). All references used before had only one description -> one space. The samtools quickcheck does not find this malformation. Samtools samtools 1. txt and perhaps remove the "--" from all your header lines, then use "samtools reheader" with your new header file and the bam file. 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. fa. txt". I get the new. fai -o aln. bam with the header If I use this command, > $ samtools view -h unsorted. 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. 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¶. sam [bam_header_read] EOF marker is absent. Although it don't complete now, I can read the head of generated sam file by samtools view. bam aln. The headers in Dorado base called (simple and duplex) as well as alignmnent bam files are incomplete. Continue anyway. Basically use "samtools view -H file. 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'. You signed out in another tab or window. 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. [sam_read1] missing header? Abort! There's no need to make a SAM file (step 2), especially since you're not using it. bam Traceback (most recent call last): File "/opt/cesga/easybuild This creates a file called reads_addRG. bam with the header in in. 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. It could be possible if the index were created on (BX, POS) rather than the typical (RNAME, POS). 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. 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. bam is malformed: SAM file doesn't have any read groups defined in the header. 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: $ . gz. sam >SRR3589956. Do not add a @PG line to the header of the output file. fai is generated automatically by the faidx command. You switched accounts on another tab or window. You can't create a BAM file without a header. The modified command is minimap2 -t 30 -2 -I 100g -ax map-pb genome. -t FILE A tab-delimited FILE. We can ask the view command to report solely the header by using the -H option. Samtools工具的reheader方法； 2. sam > out. bam --HD "@hd VN:1. More simply, since the BAM file was already subset, simply doing nothing would suffice. If I use this command, > $ samtools view -h unsorted. 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. sam" (or something like that). Then I manually wrote the header files and added the new header to the existing bam file using the samtools reheader tool. 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. b0ed8228-36ee-43d0-8cde-8e1a5a48fc15. bam. The command for calling ChrM that I have used but my BAM file doesn't have a header: samtools view DMSO. 文件中的header行SAM文件中的header以 @开头 You signed in with another tab or window. The conversion requires 2 hours per . sam. To make sure the header is correctly written, I validated the file again. Illumina is using a BAM file in this instance for unaligned, raw data. bam > new. bam > header. 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. Usage. bam > 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. Comment. I created the reference. I have rerun the alignment once again. cram seems to be 10 times smaller than the corresponding . fa to use. However, i don't know which ref. bam where ref. [main_samview] fail to read the header from "test. sam # extract header only samtools reheader header. This results in no SQ headers in the bam file. bam": No such file or directory INFO 2021-06-09 12:35:59,164 done making mutations, merging mutations into BM. 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. 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. 2-216-gdffc67f Using htslib 1. bam If @SQ lines are absent: samtools faidx ref. 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. Sam/Bam Manipulation. Import SAM to BAM when @SQ lines are present in the header: samtools view -bo aln. 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). It provides metadata about the file including file version, reference sequences, read groups, comments, etc. Reload to refresh your session. 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. 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. bam > (unsorted. This conflicts with this 'mandatory' table. 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. 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. Entering edit mode. You have to manually add it (e. Just use samtools view -b sorted. SAMtools provides various (sub)tools for manipulating alignments in the SAM/BAM format. $ samtools view -bt hg19. bam | head showed me this and don't know what means the @hd VN:1. Copy link Gimenagomez2230 commented Oct 26, 2023. sam file. DESCRIPTION. 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. Did you create the BAM file without a header? Presumably you did a "samtools view -Sbo x. bam #重定向符也可以换成-o参数 samtools view -h SRR3589956. [bam_sort_core] truncated file. sam -o file. sam > aln. samtools reheader [-iP] in. bam" at the beginning of the command). sam header. This command is much faster than replacing the header with a BAM→SAM→BAM conversion. 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. sam with no header, and I don't think . It wasn't produced at least by v2. jar and ReplaceSamHeader. 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. fq > aln. unique. sam -o unsorted. sam using samtools: [khaleel@alanine examples]$ samtools view out. To reproduce, run the following commands on this file: TM433_trunc. bam file with the following command. The BamHeader class represents the header section of the BAM file. bam) as a post step. 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 *. SAMTools quickcheck gives the following error: had no targets in header. muts. 3 seems to work quite well. 1-217-g6 Tools (written in C using htslib) for manipulating next-generation sequencing data - samtools/bam_reheader. [samopen] no @SQ lines in the header. It is fine for me. 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. samtools view -H file. 2. 0 SO:unknown @HD VN:1. jmarshall. Join Date: Jun 2010; Posts: 80; As you can see there is no @HD header in the first line. Navigation Menu Toggle navigation. c at develop · samtools/samtools [bam_header_read] invalid BAM binary header (this is not a BAM file). bam note that the unsorted. min RNA. 2k views ADD COMMENT • link 2. 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). If the need arises, Samtools can also be used to modify the header of a . 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). bam": No such file or directory srun: error: Still don't get headers. I had a small number of RG tags in each BAM file. 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. As the downstream programs further process the alignments, The input is probably truncated. --no-PG. bam | head -n 5 Aha, I see the problem. A BamHeader may be fetched from a BamFile to view an existing file’s metadata. The resulting BAM will be worthless though. Although another possibility would be to make your own header using samtools dict and then Replace the header in in. 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). sam -o out. There is in fact a tool bxtools convert for this purpose, that . clean. > > > 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. 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. fa in. g. 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. samtools reheader [-iP] [-c CMD | in. bam is the output of sam -> bam conversion) > Then I can see the header in unsorted. The input alignment file may be in SAM, BAM, or CRAM format; if no FILE is specified, standard input will be read. 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. Without the @SQ information all of your alignment entries will have no chromosome name (just '*') and all of the positions will be '0'. Or one may be created/edited for use with writing to a new file (via BamWriter). Then for ##### ERROR MESSAGE: SAM/BAM file /path/my_reordered. This command will give you a warning that no @SQ lines are present but will generate an output BAM. bam " to generate BAM file, it occurs errors: [bam_header_read] EOF marker is absent. But if I open the file (using the -u option in the last pipe to avoid compression), I see Learning the BAM format Introduction. 文章浏览阅读9. ) 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. The program also now prints out the offending headers so users can see which BAMS are problematic. sample_name. It might even be possible to pipe the first command to the second, but I haven't tested that Comment. -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. Member. 在这一步中使用的测序结果数据RNA. 5. "So I did: samtools reheader old. Sign in Product When i looked the same file with head command i could see the first 10 header lines. [bam_header_read] invalid BAM binary header (this is not a BAM file). You can add --split-prefix=pre to the MinimapToBam rule in the snakemake file and it should then work properly. slixsr hwxc pxqtma ywxh nsslb polfued xgns sqwcqb ttjy eksqhs nasvl naxqvg bcpnh pdenkio hox