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Samtools merge

samtools-merge(1) manual page - htslib

samtools merge - merges multiple sorted input files into a single output Samtools is a set of utilities that manipulate alignments in the SAM (Sequence Alignment/Map), BAM, and CRAM formats. It converts between the formats, does sorting, I am trying to merge the sorted unmapped and uniquely mapped bam files with the command. samtools merge A1_merged.bam -b A1_unmapped.bam A1_unique.bam and am

samtools(1) manual pag

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 I ran samtools merge -O CRAM --reference ref.fasta output.cram input1.bam input2.bam; Then I ran samtools sort output.cram > output.sorted.cram; Then I ran Note: Samtools' merge does not reconstruct the @RG dictionary in the header. Users must provide the correct header with -h, or uses Picard which properly maintains the samtools split now supports splitting by tag content with the -d option . samtools merge now accepts a BED file as a command line argument (-L) and does the

Samtools merge Failed to open file BAM T erro

  1. SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position
  2. Force merge for one specific strand only. Follow with + or - to force merge from only the forward or reverse strand, respectively. By default, merging is done without
  3. Samtools is a set of utilities that manipulate alignments in the BAM format. It imports from and exports to the SAM (Sequence Alignment/Map) format, does sorting
  4. rule samtools_merge: input: [mapped/A.bam, mapped/B.bam] output: merged.bam params: # optional additional parameters as string threads: # Samtools takes

Samtools - Workflow

Multiple outputs to single list input - merging BAM files in Nextflow. I am attempting to merge x number of bam files produced via performing multiple alignments at Re: [Samtools-help] samtools merge issue. From: Thomas W. Blackwell <tblackw@um...> - 2017-05-12 16:51:14. Mark - Just guessing: One may need to specify merge -f If using bamtools merge no problem. If I convert the two input bam files into sam file, then samtools merge has no problems. There must be something strange happened It would be useful if the samtools cat command merged headers (in the way that samtools merge does

[samtools]merge命令简介_睿智如水-CSDN博

merge bams file and add @RG and @CO. Let's say you have two bam files from two different runs you need to merge. bam1_batch1.bam; bam1_batch2.bam; Using samtools view -H <bamfile>, get @RG information for each of two bams.I usually get ID, DT and PL info. from bam header and then add SM (sample tag) tag using following script Hello, I am having an issue with merging different bam assemblies using samtools. In my pipeline, I merge reads using flash2, and then perform reference-based assemblies using bwa, one assembly uses just the merged reads and a second assembly uses just the unmerged reads Merging sorted files is a linear operation, so any well-implemented tools that do it will do it with approximately the same efficiency. So samtools merge (use the most up-to-date version, as there have been improvements in merge header handling in the 1.3.x and 1.4.x versions), picard MergeSamFiles, etc.. These tools need to hold all the input BAM files open simultaneously, so depending on how.

samtools merge命令 - 简

  1. Try samtools: samtools view -? A region should be presented in one of the following formats: `chr1',`chr2:1,000' and `chr3:1000-2,000'. When a region is specified, the input alignment file must be an indexed BAM file. something like samtools view in.bam chr1 > chr1.bam should wor
  2. I am trying to merge 3 .bam files (different alignments of the same ChIP-seq run), one has 5.9M reads, one 1.2M and one 0.4M. However after running merge bam files in sam tools I only get back a file with 4.2M reads in it (at least the output of rmdup tells me I have 4.2M reads). Any ideas as to why I seem to have lost 3M or so reads during merging of files? Many thanks. Dave. tool samtools.
  3. Note: Samtools' merge does not reconstruct the @RG dictionary in the header. Users must provide the correct header with -h, or uses Picard which properly maintains the header dictionary in merging. 4.index. 为了能够快速访问bam文件,可以为已经基于坐标排序后bam或者cram的文件创建索引,生成以.bai或者.crai为后缀的索引文件。必须使用排序后的.
  4. samtools merge out.bam in1.bam in2.bam in3.bam. samtools faidx ref.fasta. samtools pileup ‐f ref.fasta aln.sorted.bam. samtools tview aln.sorted.bam ref.fasta. 描述: Samtools是一系列处理BAM格式序列的应用。它从SAM(Sequence Alignment/Map)格式输入或者输出为SAM格式,可以进行排序,合并和建立索引,并且允许快速地检索任意区域的读段(reads.

Output files. The output file format mimics the input file type, with some additional fields. Note that the first 10 columns are a standard narrowPeak file, pertaining to the merged peak across the two replicates.. Column 5 contains the scaled IDR value, min(int(log2(-125IDR), 1000) For example, peaks with an IDR of 0 have a score of 1000, peaks with an IDR of 0.05 have a score of int(-125log2. samtools merge [ ] Note: 之所以会有这种情况,是因为有些样本测得非常深,其测序结果需要经过多次测序(或者分布在多个不同的测序lane中)才全部获得,这个时候我们一般会先分别进行比对并去除重复序列后再使用samtools进行合并 GAT Usage: samtools merge [-nr] [-h inh.sam] [...] 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 [in1.bam] Note: Samtools' merge does not reconstruct the @RG dictionary in the header. Users must. $ samtools merge [out. bam][in1. bam][in2. bam][in3. bam] (4)index :index alignment. 本命令对bam文件建立索引并产生后缀为.bai的文件,用于快速的随机处理。很多后续分析的过程需要有bai文件的存在,特别是显示序列比对情况下,比如samtool的tview命令等。 #必须对bam文件进行默认情况下的排序后,才能进行index.

SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. SAMtools is hosted by GitHub. The project page is here. The source code releases are available from the download page. You can check out the most recent source code with: Publications. Li H.*, Handsaker B.*, Wysoker A. samtools 的说明文档: Usage: samtools merge [-nr] [-h inh.sam] <out.bam> <in1.bam> <in2.bam>[...] 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] Note: Samtools' merge. indexBam creates an index for each BAM file specified, analogous to the 'samtools index' function. mergeBam merges 2 or more sorted BAM files. As with samtools, the RG (read group) dictionary in the header of the BAM files is not reconstructed. Details of the ScanBamParam class are provide on its help page; several salient points are reiterated here. ScanBamParam can contain a field what. The samtools merge command merges multiple sorted alignments into one output file. $ samtools merge output_alignments_merge.bam input_alignments_sorted_1.bam input_alignments_sorted_2.bam. SAMtools Faidx. The command samtools faidx indexes the reference sequence in fasta format or extracts subsequence from indexed reference sequence. $ samtools faidx input_reference.fasta . SAMtools Mpileup.

samtools用法详解_sunchengquan的博客-CSDN博

samtools 使用简述

Samtools - Documentatio

When merging intervals, we often want to summarize or keep track of the values observed in specific columns (e.g., the feature name or score) from the original, unmerged intervals. When used together, the -c and -o options allow one to select specific columns (-c) and apply operation (-o) to each column. The result will be appended to the default, merged interval output. For example, one could. Hello, The mapped datasets are based on a different reference genome (the two halves) so cannot be used in the same analysis. Much current bioinformatics computation is based on data positions relative to a common reference genome (or transcriptome, exome, etc) To be used in conjunction with samtools mpileup. This command replaces the former bcftools view caller. Some of the original functionality has been temporarily lost in the process of transition to htslib, but will be added back on popular demand. The original calling model can be invoked with the -c option. Usage: bcftools call [options] <in.vcf.gz> File format options: -O, --output-type <b.

Split and merge PDF files

  1. samtools index test.sort.bam. 4、merge. 功能:合并多个已经sort的bam文件 . 当有多个样本的bam文件时,可以使用samtools的merge命令将这些bam文件合并为一个排序的且保持所有输入记录并保持现有排序顺序的bam文件。 主要参数释义:-n:输入根据read排序的文件-r:RG标签添加到每个比对文件上,标签值来自文件名.
  2. samtools merge命令的功能描述: 当有多个样本的bam文件时,可以使用samtools的merge命令将这些bam文件进行合并为一个bam文件。Merge命令将多个已经排序后的bam文件合并成为一个排序的且保持所有输入记录并保持现有排序顺序的bam文件。若使用-h参数,则将输入文件的@SQ文件头合并到指定的文件头中
  3. Zhou in #1393) * Ampliconclip and ampliconstats now guard against the BED file containing more than one reference (chromosome) and fail when found. Adding proper support for multiple references will appear later. (#1398) ----- bcftools - changes.
  4. 测序的PCR duplicates及用samtools的rmdup去除PCR重复reads. PCR扩增加了接头的DNA片段。. 理想情况下,对打碎的基因组DNA,每个DNA片段测且仅测到一次。. 但这一步扩增了6个cycle,那么每个DNA片段有了64份拷贝。. 将扩增后所有产物洒到flowcell, 来自一个DNA片段的两个.
  5. ./samtools view -bSu Ce_align1.sam | ./samtools sort - Ce_align1_sorted ./samtools index Ce_align1_sorted.bam To make the sorting quicker you can give the argument -m with as much memory as you can spare in bytes, e.g. -m 2147483648 for 2 GB. Cheers, Samuel On 02/23/2012 09:23 PM, Kristan Steffen wrote: > Hi, > > I'm trying to use samtools to convert a .sam file to .bam so I can use.
  6. Comment(s) to include in the merged output file's header.--help -h: false: display the help message--INTERVALS -RGN: An interval list file that contains the locations of the positions to merge. Assume bam are sorted and indexed. The resulting file will contain alignments that may overlap with genomic regions outside the requested region.

samtools使用大全. samtools是一个用于操作sam和bam文件(通常是短序列比对工具如bwa,bowtie2,hisat2,tophat2等等产生的,具体格式可以在消息框输入SAM查看)的工具合集,包含有许多命令。. 以下是常用命令的介绍。. 1.View. view命令的主要功能是:将sam文件与bam文件. 01Usage: samtools merge [-nr] [-h inh.sam] <out.bam> <in1.bam> <in2.bam>[] 03Options: -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] 11 Note: Samtools' merge does not reconstruct the. samtools view sample.sorted.bam 1:33000000-34000000 | wc -l. samtools view The samtools view command is the most versatile tool in the samtools package. It's main function, not surprisingly, is to allow you to convert the binary (i.e., easy for the computer to read and process) alignments in the BAM file view to text-based SAM alignments that are easy for humans to read and process. Calling SNPs/INDELs with SAMtools/BCFtools The basic Command line. Suppose we have reference sequences in ref.fa, indexed by samtools faidx, and position sorted alignment files aln1.bam and aln2.bam, the following command lines call SNPs and short INDELs: . where the -D option sets the maximum read depth to call a SNP

SAM tools / Thread: [Samtools-help] samtools merg

The main part of the SAMtools package is a single executable that offers various commands for working on alignment data. The view command performs format conversion, file filtering, and extraction of sequence ranges. Files can be reordered, joined, and split in various ways using the commands sort, collate, merge, cat, and split. Files can. (Default: `no`) -M, --multimap Consider not unique mappings (not reccomended) -@, --samtools-threads INTEGER The number of threads to use to sort the bam by cellID file using samtools --samtools-memory INTEGER The number of MB used for every thread by samtools to sort the bam file -t, --dtype TEXT The dtype of the loom file layers - if more than 6000 molecules/reads per gene per cell are. samtools-fastq. This tool converts a BAM or cram file ino FASTQ format. The files will be automatically compressed if the file names have a .gz or .bgzf extension.. If the input contains read-pairs which are to be interlaed or written into separate files in the same order, then the input should be first collated by samtools-collate or samtools-sort by name Samtools merge 时出错: 弄了个软链接,如图2,使用链接过去的文件时出现图1的错误,主要是软链接的时候没有全部提供绝对路径。 出现以下错误,是因为事先没提前对bam文件进行sort,genomeCoverageBed中的输入文件同样需要经过排序,如若是bed,则须用sort排序,如若是bam,则用samtools sort进行排序

samtools常用命令详解 - emanlee - 博客

samtools-split - Man Page. splits a file by read group. Synopsis. samtools split [options] merged.sam|merged.bam|merged.cramDescription. Splits a file by read group, producing one or more output files matching a common prefix (by default based on the input filename) each containing one read-group samtools index test.sort.bam . 4、merge. 功能:合并多个已经sort的bam文件 . 当有多个样本的bam文件时,可以使用samtools的merge命令将这些bam文件合并为一个排序的且保持所有输入记录并保持现有排序顺序的bam文件。 主要参数释义:-n:输入根据read排序的文件-r:RG标签添加到每个比对文件上,标签值来自文件. I have some problems in creating a .bed file for hg19, so I will be able to visualize the .bed file in IGV. The .fasta file contains rows of this form: >chr1:0-100 In general, if you want to compute a p value on anything you need separate replicates (not merged). If you are just annotating peaks you don't need a p value. how to pool together biological replicates? ChipSeq: merge bam file before peak calling. Chip-Seq merging peak files. And merging BAM can be done using samtools Merge multiple sorted alignment files, producing a single sorted output file that contains all the input records and maintains the existing sort order

samtools merge out.bam in1.bam in2.bam in3.bam samtools faidx ref.fasta samtools fixmate in.namesorted.sam out.bam samtools mpileup -C50 -gf ref.fasta -r chr3:1,000-2,000 in1.bam in2.bam samtools tview aln.sorted.bam ref.fasta samtools flags PAIRED,UNMAP,MUNMAP samtools bam2fq input.bam > output.fastq DESCRIPTION - 描述. Samtools是一个用来处理BAM格式(SAM的二进制格式,译者. Index bam file with samtools. For more information see # Samtools takes additional threads through its option -@ # One thread for samtools merge # Other threads are *additional* threads passed to the '-@' argument threads = if snakemake. threads <= 1 else -@ {} . format (snakemake. threads-1) shell (samtools index {threads} {snakemake.params} {snakemake.input[0]} {snakemake.output[0.

NeatSeq-Flow Tutorial Workflow — NeatSeq_Flow ModuleUnaligned BAM to BQSR and VCF - Common Workflow Language

PDF SAM (PDF Split and Merge) 4.2.6 - kostenloser Download / Deutsch - PDF SAM dreht, teilt und fügt Ihre PDF-Dateien frei nach Ihren Wünschen zusammen NAME¶ sambamba-merge - tool for merging several BAM files into one SYNOPSIS¶ sambamba merge OPTIONS <output.bam> <input1.bam> <input2.bam> [...] DESCRIPTION¶ sambamba merge is used for merging several sorted BAM files into one. The sorting order of all the files must be the same, and it is maintained in the output file samtools merge -@ 8 output.bam input1.bam input2.bam input3.bam. 2つ以上のbam、samを1つにまとめる。split コマンドでクロモソームごとに分割し、別のクラスターでランして、後で統合するような用途にも使えそうである。 split- sam/bamの分割. samtools split fasta - bam/samからfastaを 抽出. samtools fasta input.bam > input.fa fastq. merge: マージする。 13: rmdup: PCRによる重複を除去する。 SAMtoolsにはSNP解析用の各種オプションが用意されています。 ここでは一例としてマップされたサンプルタグのコンセンサス塩基を表示する-cオプションの指定例を示しています。 samtools pileup aln.bam -f ref.fa -c | awk 'toupper($3)!=toupper($4)&&$9. I'm trying to install samtools on openSUSE, I did this: cd htslib-1.2.1 ./configure make install Worked fine. bcftools-1.2 ./configure make install Worked fine. And for samtools: cd samtools-..

samtools merge CRAM output · Issue #1494 · samtools

Hier hilft ein PDF-Editor wie PDFsam für Windows, Linux und macOS, der PDF-Dateien zusammenfügen oder zerschneiden kann, also merge und split beherrscht, wie es im Englischen heißt. 'samtools merge' can add the RG field for you, it will assume one read group per input file. It's your responsibility to provide a BAM header that actually defines these read groups, so you'd probably run 'samtools merge' followed by 'samtools reheader'. See the BAM documentation for the correct format of the RG lines. ADD COMMENT • link 9.7 years ago by Marvin ▴ 850 Login before. Rsamtools-package 'samtools' aligned sequence utilities interface Description This package provides facilities for parsing samtools BAM (binary) files representing aligned se-quences. applyPileups 3 Details See packageDescription('Rsamtools')for package details. A useful starting point is the scanBam manual page. Note This package documents the following classes for purely internal. samtools view tmp.sort.bam . 3.merge和cat. merge将多个已经sort了的bam文件融合成一个bam文件。融合后的文件不需要则是已经sort过了的。而cat命令不需要将bam文件进行sort。 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.

samtools的merge功能在合并之后,输出的文件也是保持着原来的顺序,即sort的顺序,所以你不用再次sort。 在merge后,再次检查mapped reads数(我是把8个文件两两合并): merge_1.bam mapped_reads_number 41960112 merge_2.bam mapped_reads_number 25290502 merge_3.bam mapped_reads_number 36771804 merge_4.bam mapped_reads_number 25911388 . 发布于. samtools rmdup [-sS] <input.srt.bam> <out.bam>. 只需要开始-s的标签, 就可以对单端测序进行去除PCR重复。. 其实对单端测序去除PCR重复很简单的~,因为比对flag情况只有0,4,16,只需要它们比对到染色体的起始终止坐标一致即可,flag很容易一致。. 但是对于双端测序就有点. samtools merge out.bam in-1.bam in-2.bam で in-1.bam および in-2.bam という 2 つのファイルがマージされる。この部分は *.bam でも大丈夫。 fastq. samtools fastq input.bam > output.fastq のようにして、bam から fastq ファイルを作るのに使う。詳細はページ下方の bam から fastq への変換 を参照のこと。-h. ヘッダーを維持.

samtools常用命令详解 - 简

samtools merge out.bam in1.bam in2.bam in3.bam samtools faidx ref.fasta samtools pileup ‐f ref.fasta aln.sorted.bam samtools tview aln.sorted.bam ref.fasta 描述: Samtools是一系列处理BAM格式序列的应用。它从SAM(Sequence Alignment/Map)格式输入或者输出为SAM格式,可以进行排序,合并和建立索引,并且允许快速地检索任意区域的读段(reads. Background: Currently samtools only parses part of the SAM header, which causes problems in maintaining a proper header in merging, sorting and several other operations. Description : Write a set of rountines that parse the SAM header into a dictionary structure, write the dictionary into the SAM header format, merge dictionaries, add or remove tags and so on samtools view sample.bam \ chr6:28477797-33448354 chr6_apd_hap1:1-4622290 \-b > sample.HLA.bam samtools view sample.bam -bh-f 12 -@ 8 > sample.unmapped.bam samtools merge sample.merge.bam sample.HLA.bam sample.unmapped.bam samtools sort-n sample.merge.bam -@ 8 -o sample.sort.bam samtools fastq sample.sort.bam \-1 sample.HLA.R1.fastq \-2 sample.HLA.R2.fastq \-s /dev/null \-@ # include reads that map to the reverse strand (128) # and are second in a pair (16): 128 + 16 = 144 $ samtools view -b -f 144 a.bam > a.rev1.bam # include reads that are first in a pair (64), but # exclude those ones that map to the reverse strand (16) $ samtools view -b -f 64 -F 16 a.bam > a.rev2.bam # merge the temporary files $ samtools merge -f rev.bam a.rev1.bam a.rev2.bam # index the.

Releases · samtools/samtools · GitHu

First, samtools mpileup command transposes the mapped data in a sorted BAM file fully to genome-centric coordinates. It starts at the first base on the first chromosome for which there is coverage and prints out one line per base. Each line has information on every base observed in the raw data at that base position along with a lot of auxiliary information depending on which flags are set. It. If bamtools merge does not work for you (there seem to be version specific problems), you can alternatively try using samtools for the same purpose (this suggestion was reported by Philipp Schiffer, thank you!) 使用samtools view命令再试试看? 4. 使用samtools sort命令对test.bam文件进行排序,输出文件名为test_sort.bam,并记录文件大小。 5. 使用samtools index 对test_sort.bam建立index,写出命令并记录其文件大小。 6. 使用samtools tview使用下面的命令查看chr1:160000-160100区域的比对情况. SAMtools is a library and software package for parsing and manipulating alignments in the SAM/BAM format. It is able to convert from other alignment formats, sort and merge alignments, remove PCR duplicates, generate per-position information in the pileup format ( Fig. 1 c), call SNPs and short indel variants, and show alignments in a text-based viewer samtools allows you to sort based on certain flags that are specified on page 4 on the sam format specification. We'll focus on a couple, below. Here are three of the most useful flags to sort on. We'll be using the unmapped flag. a few samtools flags # SAM specifications common flag usage 0x04 = unmapped 0x02 = part of a properly aligned pair 0x400 = optical duplicate # look at samtools rmdup.

SAMtool

merge — bedtools 2

Samtools at GitHub is an umbrella organisation encompassing several groups working on formats and tools for next-generation sequencing: File-format specifications. The hts-specs repository contains the specifications of several sequence data formats (SAM, BAM, and CRAM), variant calling data formats (VCF and BCF), and related formats such as indices. Changes to these formats are discussed as. SAMTOOLS DEPTH¶. Compute the read depth at each position or region using samtools. For more information see SAMtools documentation.. URL Notes¶. Samtools -@ /-threads takes one integer as input. This is the number of additional threads and not raw threads

Ubuntu Manpage: samtools - Utilities for the Sequence

847M Jul 28 17:05 Control.merge.bam 1.3G Jul 28 17:06 H2Aub1.merge.bam 834M Jul 28 17:06 H3K36me3.merge.bam 1.5G Jul 28 17:08 RNAPII_S2P.merge.bam 831M Jul 28 17:09 RNAPII_S5P.merge.bam 218M Jul 28 17:09 RNAPII_S5PRepeat.merge.bam 722M Jul 28 17:09 RNAPII_S7P.merge.bam 472M Jul 28 17:10 Ring1B.merge.bam. 14个fq测序数据只剩下8个样本. Migrate and merge conflicting objects; Uncheck Before merging remove user rights for existing target account - I have some pre-assigned groups and don't want to remove those. select Move merged objects to the specified target Organizational Unit - I am moving user objects from a pre-created OU to Migrated OU after the migration. 12 Blackboard dominated the U.S. learning management system market for 20 a software company that later merged with Blackboard LLC to form 11. SHSU Online Awards and Recognition

P000000939_en

Picard-like SAM header merging in the merge tool; Optional [==> ] for operations on whole BAMs; Fast copying of a region to a new file with the slice tool; Duplicate marking/removal, using the Picard criteria; And, of course, the biggest one (yeah, literally!), PERFORMANCE Benchmarks. Indexing 17GB file on 8 cores, HDD real time, s: user time, s: sambamba: 31: 69: samtools: 70: 67: Copying. Unlike C-compiled programs such as Samtools, Picard cannot simply be added to your PATH, so we recommend setting up an environment variable to act as a shortcut. For the tools to run properly, you must have Java 1.8 installed. To check your java version by open your terminal application and run the following command: java -version . If the output looks something like java version 1.8.x, you.

chapter44-45 illumina和PacBio仪器简介 - 简书

Ø samtools rmdup -S input.bam out.bam ## input.bam had paired data 1. I see about 20% reduction in reads. Does this point to a problem in PCR step or this is within the normal range. 2. Also wondering why initial samtools flagstat on orig bam file doesn't output the #duplicates 3. I hope my understanding of this process is correct. I think all. Note. bedtools multicov depends upon index BAM files in order to count the number of overlaps in each BAM file. As such, each BAM file should be position sorted (samtool sort aln.bam aln.sort) and indexed (samtools index aln.sort.bam) with either samtools or bamtools

module load samtools/1.3.1 samtools Program: samtools (Tools for alignments in the SAM format) Version: 1.3.1 (using htslib 1.3.1) Usage: samtools <command> [options] Commands: -- Indexing dict create a sequence dictionary file faidx index/extract FASTA index index alignment -- Editing calmd recalculate MD/NM tags and '=' bases fixmate fix mate information reheader replace BAM header rmdup. BWA and SAMTOOLS •Set up tools and data $ module load bwa/0.7.4 $ module load samtools/0.1.19 $ cp reference_genome.fasta bwa_reference_genome.fasta $ mkdir bwa_mapping_assembly $ cd bwa_mapping_assembly $ newMapping mapping_assembly •Set the reference sequence and read data $ set best_refs_file =./bwa_reference_genome.fasta $ set final_sff_fastq =./unknown_norovirus_454_convert.fastq. Multiple tools are available for sorting and indexing BAM files, including igvtools, the samtools package, and in GenePattern. The GenePattern module for sorting and indexing is Picard.SortSam. SAM files can be sorted and indexed using igvtools. Note: The .SAI index is an IGV format, and it does not work with samtools or any other application SAMtools did better in memory utilization, steadily consuming ~ 50 Gb memory after ramping up. While running SAMtools, we provisioned only 45 Gb (1.5 Gb for each of the 30 threads) so one should only specify 80-90% of available memory to SAMtools. Sambamba used close to the 45 Gb memory we specified for the first 5 minutes before dropping the. samtools view -Su alns.sam | samtools sort - alns.sorted The file resulted from the above command ( alns.sorted.bam ) can be used as input for StringTie. Every spliced read alignment (i.e. an alignment across at least one junction) in the input SAM file must contain the tag XS to indicate the genomic strand that produced the RNA from which the read was sequenced

WGS全流程的学习笔记 - 简书

SAMTOOLS MERGE — Snakemake Wrappers tags/0

Heterochromatin-Enriched Assemblies Reveal the SequenceAnnotation for DNA polymorphism (DNApod workflow) - VMWhole-genome Identification of Transcriptional Start Sites