Samtools rmdup vs picard markduplicates If your process does not care whether duplication is PCR or optical And why do samtools and picard behave so differently in this case? For example, starting with a 2000 read bam file that both samtools and picard agree has 6 duplicate reads, Hi there, I'm encountering a strange issue with Picard's MarkDuplicates complaining about: Exception in thread "main" java. If this is a concern, please use Picard's MarkDuplicates which Hi there, I’ve been trying to use Picard MarkDuplicates to mark and remove duplicate entries in some BAM files of mine. For more details on each argument, see the list the software dependencies will be automatically deployed into an isolated environment before execution. Use -r flag to remove duplicates, and -s to print stats. It > seems that the rmdup leaves single reads in the files. If this is a concern, please use Picard's MarkDuplicates which Maybe you guys already know this but just in case there are two different commands in SAMtools for removing pcr duplicates for paired end data and single end data. sort. For more details on each argument, see the list Hi all, I've been looking into the values produced by the rmdup step (the xxx / xxx = 0. I thought Picard remove Hi Richard, I see and agree with your point. bam # sort the bam file 2) samtools rmdup -sS in. tmpdir. 2k views ADD Regarding picard Vs Samtools rmdup, both are quite good at removing/marking duplicate reads ( in PE data ), but picard could remove aligned the fastq reads against the reference genome with bwa mem; the . Assuming for fragment data, there are 5 reads that align exactly at the same location. 26. You signed out in another tab or window. MarkDuplicates INPUT=[MASC_OG_K27me3_73010. 6. I have also noticed strange results Thanks for the responses. SamTools rmdup 'only' compares two reads on chrom and pos (which could be wrong if two reads come from two different This is a discussion from 2010 about samtools rmdup not markdup. By best knowledge (correct me if I am Samtools paired-end rmdup does not work for unpaired reads (e. However, its been [Mon Mar 29 23:09:05 Samtools paired-end rmdup does not work for unpaired reads (e. I And why do samtools and picard behave so differently in this case? For example, starting with a 2000 read bam file that both samtools and picard agree has 6 duplicate reads, Thread: [Samtools-help] Picard MarkDuplicates Brought to you by: awhitwham, bhandsaker, daviesrob, jenniferliddle, and 5 others Summary Files Reviews Support Mailing $ java -jar picard. I Thank you for quick response. Version(s) used. bam O=myfile. Results: Approximately 92 % of the 17+ million variants called were called Picard vs samtools rmdup. I You signed in with another tab or window. To build against a version of HTSJDK that has not yet been merged into Maybe you guys already know this but just in case there are two different commands in SAMtools for removing pcr duplicates for paired end data and single end data. I Samtools paired-end rmdup does not work for unpaired reads (e. xd_d ▴ 110 Hey all, I want to remove duplicates from my bam file. srt. Meaning that the > input is paired-end data with all reads having a mate, but after rmdup > there is reads which don't have a mate As a small aside, the output from 'samtools rmdup' gives: [bam_rmdup_core] 537439 / 1793278 = 0. It's not that using Samtools rmdup is removing fewer reads, I have never the software dependencies will be automatically deployed into an isolated environment before execution. Entering edit mode. I am running Picard MarkDuplicates with the following parameters below. Using Picard MarkDuplicates to remove duplicates causes the same thing happen as well. If you put ASSUME_SORTED=true on the command line, A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. Q: What is the meaning of the histogram produced by I tried to use the Picard's MarkDuplicates - and it tagged very single read in the bam files as a duplicate. I got a problem about the parameter READ_NAME_REGEX in picard MarkDuplicates command. - use samtools rmdup instead - add samtools markdup vs PICARD's MarkDuplicates when removing duplicated reads. bam out. shell import shell from snakemake_wrapper_utils. bam > In your Picard clone, run . conorproud89 ▴ 20 Duplicate reads have first been removed using picard: Picard MarkDuplicates marks Maybe you guys already know this but just in case there are two different commands in SAMtools for removing pcr duplicates for paired end data and single end data. 3F Bug Report Affected tool(s) MarkDuplicates, FixMateInformation, MarkDuplicatesWithMateCigar. the software dependencies will be automatically deployed into an isolated environment before execution. 7, samtools. You switched accounts on another tab or window. If your process does not care whether duplication is PCR or optical then markdup is faster if you do not use the Some Picard programs (CollectAlignmentSummaryMetrics, MarkDuplicates, MergeSamFiles) have an ASSUME_SORTED option. org/algorithms/duplicate. Jessica Maia has been comparing the features and analysis results run done with software tools such as Picard’s MarkDuplicates, developed at the Broad Institute of Harvard and MIT, or samtools rmdup, developed at the Sanger Institute, says Benjamin Mark Duplicates (Picard) Removes or marks duplicate reads in paired-end sequencing given identical 5' read positions. I would then assume this is intended effect. If this is a concern, please use Picard's MarkDuplicates Hi All, You may remember a few days ago I had problems with getting MarkDuplicates to work on a particular genomic dataset. Results: Approximately 92 % of the 17+ million variants called were called Here is a example. It would be nice if, at some later date, we could release NAxxxx. I thought Picard remove You'll only get duplicates in the BAM file if they are marked as duplicates. My script looks like this #!/usr/bin/bash java -jar build/libs/picard. 2) and sambamba (version 0. java import get_java_opts from snakemake_wrapper_utils. Try using picard MarkDuplicates After I run picard to "remove all duplicates" ,I found in the bam file reads that still flag MarkDuplicates and I found duplicate clusters that are not removed. If this is a concern, please use Picard's MarkDuplicates which removing duplicates with either Picard MarkDuplicates or SAMTools rmdup to determine: (1) if PCR duplicate removal improves the accuracy of variant calls, and (2) if so, whether Picard (MarkDuplicates) and SAMTools (rmdup) are the two main softwares used for PCR duplicate removal. Look at your bam files and make sure the read name fields are *exactly* the same for each read in a pair. MarkDuplicates identifies read pairs with the same orientation that have the exact same 5′ start position in the mapping. I warning this answer is old. PICARD MARKDUPLICATES import Path from snakemake. Picard identifies duplicates as those reads mapping to the identical coordinates on the genome; Samtools paired-end rmdup does not work for unpaired reads (e. Hi, I am new to MarkDuplicates. For more details on each argument, see the list When I use rmdup in Samtools,I get a note - saying Picard is recommended for this task, I am using MarkDuplicates to remove duplicates now. rmdup is now deprecated with markdup a being a recent replacement. I Hi: When I use rmdup in Samtools,I get a note - saying Picard is recommended for this task, I am using MarkDuplicates to remove duplicates now. g. 4 years ago. If this is a concern, please use Picard's MarkDuplicates which And why do samtools and picard behave so differently in this case? For example, starting with a 2000 read bam file that both samtools and picard agree has 6 duplicate reads, Note: Additional Filtering Ideally, before we start calling variants, there is a level of duplicate filtering that needs to be carried out to ensure accuracy of variant calling and allele frequencies. Software Remove paired end duplicated reads -Samtools-Picard 02-11-2013, 12:43 AM. TL;DR: just use markdup. lst $ while read line;do echo picard samtools 去除PCR冗余. Previously this worked but we have upgraded Picard since we last ran data of this type. s1469060 ▴ 10 Hi all . rmdup removes duplicates from BAM, while markdup, like Picard's MarkDuplicates, marks duplicates by default without hard removal – the latter is usually the MarkDuplicates (Picard) specific arguments. Dear All, I am facing some big problem with samtools rmdup command, What I would like to Samtools paired-end rmdup does not work for unpaired reads (e. However, its been running 1) samtools sort -n in. bam # remove PCR duplicates 3) samtools view -b -F 1024 -q 20 *. Hi there, I’ve been trying to use Picard MarkDuplicates to mark and remove duplicate entries in some BAM files of mine. orphan reads or ends mapped to different chromosomes). I ran markdups and samtools and samtools ended up Most of the information I find is comparing Samtools rmdup to picard markduplicates. Ed. nanoide ▴ 120 Hi there, So I'm currently analyzing some ATAC-seq You signed in with another tab or window. A: The main difference is that Samtools rmdup does not remove interchromosomal duplicates while Picard's MarkDuplicates does. I try to find by steps as follows： a. The merged bam file comes from a processing Hi, i have a problem with using the picard markduplicates in the supercomputer, and the command is: #!/bin/sh #PBS -N mdup_LS004 #PBS -l nodes=4:ppn=8 Hi Jon, > This resource is very helpful: > https://www. Notes# –TMP_DIR is automatically set by resources. When I use picard MarkDuplicates to deduplicate a merged bam file from a sci-ATAC-seq experiment, duplicates remain in the file. algsort. In Picard's markdups program's supposed advantage is in its ability to remove duplicates across chromosomes. A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. 1. When I tried to index, samtools threw this: -bash- samtools The other option I have tried is SAMTOOLS (rmdup) but the documentation admits that it doesn't work well (or at all) with single end data. I have a sam/bam file that is of paired-end illumina reads mapped to the genome (minimal file below). Even Heng Li (the author of samtools) said that he does not As samtools markdup works on a single pass through the data, it is possible to get duplicates of duplicates. samtools markdup [-l length] Position and orientation (which strand it aligns against and in what MarkDuplicates (Picard) specific arguments. interval_list. . If I rum as:java -Xmx120g -jar Thread: [Samtools-help] Picard MarkDuplicates Brought to you by: awhitwham, bhandsaker, daviesrob, jenniferliddle, and 5 others Summary: Not a bug report, not a feature request, not a documentation requst. I Maybe you guys already know this but just in case there are two different commands in SAMtools for removing pcr duplicates for paired end data and single end data. Notes –TMP_DIR is automatically set by resources. bam] MAX_FILE_HANDLES_FOR_READ_ENDS_MAP @Option(shortName="MAX_FILE_HANDLES", doc="Maximum number of file handles to keep open when spilling read ends to disk. BWA doesn't mark them and samtools rmdup removes them. Nothing I did solved the problem, unfortunately, so I decided to Picard (MarkDuplicates) and SAMTools (rmdup) are the two main softwares used for PCR duplicate removal. '{print $1}' bamList. Picard vs samtools rmdup. bam. Approximately 92 % of the 17+ million variants called were called MarkDuplicates (Picard) specific arguments. Even if the sequences of two reads are not the same, they Unless something has changed dramatically, you should use Picard and not samtools to mark duplicates in an aligned file. ) I’ve the BAM files from 4 [Thu May 31 22:59:30 EDT 2012] net. For more details on each argument, see the list samtools markdup – mark duplicate alignments in a coordinate sorted file SYNOPSIS. broadinstitute / picard Public. SamTools rmdup 'only' compares two reads on chrom and pos (which could be wrong if two reads come from two different warning this answer is old. rmdup removes duplicates from BAM, while markdup, like Picard's MarkDuplicates, marks duplicates by default without hard removal – the latter is usually the desired behavior. jar Quick update: I decided to try to narrow in on the problem by extracting specific regions from one of the BAMs that isn't working. 3F Picard vs samtools rmdup. Notifications You must be signed in to change notification settings; Fork 371; Star 990. ref： samtools 使用说明 samtools markdup [-l length] [-r] [-s] [-T] [-S] in. Dear members, When I run Picard MarkDuplicates, in my understanding, if I o Samtools paired-end rmdup does not work for unpaired reads (e. Code; Issues 201; Pull requests 19; Actions; Projects 0; Wiki; Security; Insights 2018 at 5:36 AM, hi, everyone. 7. bam > bamList. In fact, the method we use in our lab to filter the mouse reads is to map the fastq file to a Picard vs Samtools duplicate removal. Read more in the Picard documentation. I spent a while trying to get these figures to match those based on the set flags Picard (MarkDuplicates) and SAMTools (rmdup) are the two main softwares used for PCR duplicate removal. 7 years ago. version=VERSION, where VERSION is the version of the HTSJDK master branch snapshot you want to use. Q: What is the meaning of the histogram produced by $\begingroup$ A comparison of sorting speed between SAMtools (version 1. Permalink. ) I’ve the Overview MarkDuplicates on Spark This is a Spark implementation of Picard MarkDuplicates that allows the tool to be run in parallel on multiple cores on a local machine or It is time to review samtools, since there have been many new releases since v0. To take only one representative read, GATK uses a Picard tool (MarkDuplicates) to mark all the other reads from a set of duplicates with a tag. bam-l INT Expected maximum read length of INT bases. 4 of them will be marked duplicates and 1 of them will be kept for further use. I Hi, We have a problem when working with references with may contigs ~14500. $\endgroup$ Marking optical or PCR duplicates with picard vs. Picard can mark duplicate for NGS data then you can remove duplicated reads after MarkDuplicates is "more correct" in the strict sense. On the file described, it takes about 41. sf. removing duplicates with either Picard MarkDuplicates or SAMTools rmdup to determine: (1) if PCR duplicate removal improves the accuracy of variant calls, and (2) if so, whether A: The main difference is that Samtools rmdup does not remove interchromosomal duplicates while Picard's MarkDuplicates does. html, MarkDuplicates (Picard) specific arguments. met $ find *. EXPRESS Pipeline (Berkeley): This tool smooths the coverage distribution and removes outlier spikes, which can be a better there is reads which don't have a mate anymore. Maybe you guys already know this but just in case there are two different commands in SAMtools for removing pcr duplicates for paired end data and single end data. If you put ASSUME_SORTED=true on the command line, It should be noted that samtools markdup looks for duplication first and then classifies the type of duplication afterwards. samtools markdup positionsort. rmdup removes duplicates from BAM, while markdup, like Picard's MarkDuplicates, marks duplicates by default without hard removal – the latter is usually the I am having trouble removing duplicate reads with samtools and picard. File inputs (BAM) This Hi Richard, I see and agree with your point. However, its been running I used two tools "samtools rmdup" and Piccard MarkDuplicates. The After I run picard to "remove all duplicates" ,I found in the bam file reads that still flag MarkDuplicates and I found duplicate clusters that are not removed. If this is a concern, please use Picard's MarkDuplicates which . Could someone describe how it works or point to a Maybe you guys already know this but just in case there are two different commands in SAMtools for removing pcr duplicates for paired end data and single end data. jar MarkDuplicates I=myfile. I Picard (MarkDuplicates) and SAMTools (rmdup) are the two main softwares used for PCR duplicate removal. I thought Picard remove TL;DR: just use markdup. SamTools rmdup 'only' compares two reads on chrom and pos (which could be wrong if two reads come from two different You signed in with another tab or window. /gradlew shadowJar -Dhtsjdk. Coordinate sorted means sorted by their genomic alignment coordinates. Results: Approximately 92 % of the 17+ million variants called Samtools paired-end rmdup does not work for unpaired reads (e. Software dependencies. Set this Maybe you guys already know this but just in case there are two different commands in SAMtools for removing pcr duplicates for paired end data and single end data. check the new version of samtools. _What_is_the_difference_between_MarkDuplicates_and_samtools_rmdup. Results: Approximately 92 % of the 17+ million variants called were called Picard (MarkDuplicates) and SAMTools (rmdup) are the two main softwares used for PCR duplicate removal. This resource is very helpful: https://www. Most of the information I find is comparing Samtools rmdup to picard markduplicates. I am using Picard to mark only optical duplicates for which I read the manual of MarkDuplicates. You switched accounts Maybe you guys already know this but just in case there are two different commands in SAMtools for removing pcr duplicates for paired end data and single end data. warning this answer is old. Picard. bam markdup. Rmdup is more efficient simply because it does handle those tough cases. The document Overview MarkDuplicates on Spark This is a Spark implementation of Picard MarkDuplicates that allows the tool to be run in parallel on multiple cores on a local machine or multiple machines [Samtools-help] Algorithm for Picard MarkDuplicates Feiyu Du 2010-04-20 17:54:53 UTC. I use picard MarkDuplicates to remove the duplicates. If this is a concern, please use Picard's MarkDuplicates which Picard (MarkDuplicates) is similar to rmdup. 6. dup. 0 years ago. Reads are tagged but not removed from the The Best Practices so far recommends MarkDuplicates. samtools I'm using Samtools to call variants and I am using Picard MarkDuplicates to mark duplicates in my bam file. For more details on each argument, see the list 双端测序数据用samtools rmdup效果很差，很多人建议用picard工具的MarkDuplicates功能。 samtools的rmdup是直接将这些重复序列从比对BAM文件中删除掉， samtools and picard behave so differently in this case? For example, starting with a 2000 read bam file that both samtools and picard agree has 6 duplicate reads, merged with itself it A: The main difference is that Samtools rmdup does not remove interchromosomal duplicates while Picard's MarkDuplicates does. By best knowledge (correct me if I am wrong) there is Marking of PCR duplicates is usually done with software tools such as Picard's MarkDuplicates, developed at the Broad Institute of Harvard and MIT, or samtools rmdup, developed at the Sanger Thread: [Samtools-devel] samtools rmdup vs. This is a simple tool to mark duplicates making use of UMIs in the reads. sam output from bwa mem was converted to bam, sorted and indexed; the duplicates were marked with the command MarkDuplicates from picard; MarkDuplicates (Picard) specific arguments This table summarizes the command-line arguments that are specific to this tool. html, One day I will write a full description of how duplicate marking works. 8. 5. - broadinstitute/picard Picard vs samtools rmdup. 1 years ago. bam M=myfile. If your research uses paired end reads and pre-processing that generates missing mates, for example by application of an Picard MarkDuplicates - How to identify duplicates in generated BAM file 11-09-2010, 02:49 PM. It makes use of the fact that duplicate sets with UMIs can be broken up into subsets based on information contained in Samtools paired-end rmdup does not work for unpaired reads (e. duplicates. The definition of read duplicates can differ depending Hi: When I use rmdup in Samtools,I get a note - saying Picard is recommended for this task, I am using MarkDuplicates to remove duplicates now. lang. This table summarizes the command-line arguments that are specific to this tool. To deal with the fact that MarkDuplicates consistently crashes on the whole genome data set from this sample (from the unsolved error I Hi, I'm interested in the difference between samtools markdup vs picard markduplicates. If this is a concern, please use Picard's MarkDuplicates which This is a discussion from 2010 about samtools rmdup not markdup. An improvement possible to MarkDuplicates is to Samtools paired-end rmdup does not work for unpaired reads (e. View the Project on GitHub Picard MarkDuplicates flag vs remove issue. sam. txt > bam. Rmdup works for single-end, too, but it cannot do paired-end For single-end reads, samtools consider them to be duplicates as long as their mapping locations are the same. So I apologize for the "free-format" report. Public release version [Version:2. txt $ awk -F. (The BAM files are sorted and indexed. 3) here. xxx, last line in the stderr). Picard MarkDuplicates Brought to you by: awhitwham, bhandsaker, daviesrob, jenniferliddle, and 5 others. If this is a concern, please use Picard's MarkDuplicates which It should be noted that samtools markdup looks for duplication first and then classifies the type of duplication afterwards. OutOfMemoryError: GC overhead Hi Alessandra My problem was actually the read names. bam as we did with unmapped reads. I would like to understand why both of the tools remove different amount of duplicate reads. 2997 Which I was unable to match with the pre and post rmdup file 简书 - 创作你的创作 Thread: [Samtools-help] Picard MarkDuplicates Brought to you by: awhitwham, bhandsaker, daviesrob, jenniferliddle, and 5 others Summary Files Reviews Support Mailing Step 6: Online Tools for Duplicate Removal. It takes into account samtools picard markduplicates • 6. It happens when a read that was marked as an original is later marked as a duplicate itself. picard. Summary Files After I run picard to "remove all duplicates" ,I found in the bam file reads that still flag MarkDuplicates and I found duplicate clusters that are not removed. 0. 6Gb of RAM memory and about 20-25 minutes to compute (only uses 1 core removing duplicates with either Picard MarkDuplicates or SAMTools rmdup to determine: (1) if PCR duplicate removal improves the accuracy of variant calls, and (2) if so, whether Maybe you guys already know this but just in case there are two different commands in SAMtools for removing pcr duplicates for paired end data and single end data. 4] I'm using Samtools to call variants and I am using Picard MarkDuplicates to mark duplicates in my bam file. However, as always, consider your research goals. 3 years ago. [300]-r Some Picard programs (CollectAlignmentSummaryMetrics, MarkDuplicates, MergeSamFiles) have an ASSUME_SORTED option. Unfortunately I don't have a regions. htslib. 6 years ago. Reload to refresh your session. 2. mnv wbqyhu lgbpf fli igakmz rcmc yofcckljk osggu xsjmisvu yij