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Hello bioinformaticians, I run this code to install bam-readcount: cd $RNA_HOME/student_tools/ export SAMTOOLS_ROOT=$RNA_HOME/student_tools/samtools-1.9 git clone https://github.com...genome/bam-readcount.git cd bam-readcount cmake -Wno-dev $RNA_HOME/student_tools/bam-readcount make After a quite long-running, I...Making all in lib CCLD libcurl.l…

bam-readcount

updated 20 months ago • Chris

I'm installing bam-readcount for my analysis. However, when I came to the last step in executing the command "make", error appeared as: bamreadcount.cpp...17: fatal error: sam.h: No such file or directory compilation terminated. make[2]: * [build/src/exe/bam-readcount/CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o] Error 1 make[1]: * [build/src/exe/bam-readcount/CMakeFiles/bam

updated 11.0 years ago • waihungh

Hi, I am using bam-readcount. However, when I run the following input I get a blank output; $ bam-readcount -f NCBI_ReferenceGenome.fna -l decomposed.vcf...script, I get the following; Minimum mapping quality is set to 0 Expect library: Bowtie2 in BAM The documentation says the output should be a tab-delimited file with column names, however output.readcount is empty...and am not …

sam bam-readcount bam

updated 2.4 years ago • D_Jens

Hi All, I am trying to run bam-readcount but I get the following error in the "make" step of the installation. I am using cmake v3.4.3 The commands I used...are: >git clone https://github.com/genome/bam-readcount.git >cmake bam-readcount/ > make Error: > [ 82%] Linking CXX executable ../../../../bin/bam-readcount > …

bam-readcount

updated 6.7 years ago • hsbinf

I just downloaded and installed bam-readcount. I was checking the version bam-readcount -v bam-readcount version: 0.7.4-unstable-34-5bbd404 (commit 5bbd404...the current one to use (I cloned the git repository) git clone https://github.com/genome/bam-readcount.git I know this isn't a bioinformatics question per se, but the faq said to post here. Thank you

ngs bam-readcount

updated 8.0 years ago • bioguy24

I've noticed that the output for bam-readcount sometimes has bases in uppercase, sometimes lowercase. This is in the reference column, and also for additional...an indel is even given in mixed case (like "aaaTT"). What is the significance of case in the bam-readcount output

next-gen bam-readcount

updated 21 months ago • prograde

By reading the documentation I get the impression that the `-p` switch is for running bam-readcount on multiple libraries in one go, i.e. multiple BAM files. However, I can't really figure out whether I'm supposed

bam-readcount

updated 2.0 years ago • philip.jonsson

Hello I am trying to run bam-readcounts and fpfilter.pl on my VarScan2 output but most of my variants "failed to get readcounts for variant allele...upper cases (as was mentioned in another forum). Any idea what might be the problem? Thanks! Anat `bam-readcounts` command line: ``` bam-readcount \ -q 1 \ -b 20 \ -f /media/Data/Anat_Data/Ref_genome/human_g1k_v37.fasta \ no_R2_mapped_s…

bam-readcounts VarScan2

updated 2.0 years ago • anat

Hi all, I want to use bam-readcount pipeline, so I followed the instruction and installed it. When I tried to use bam-readcount to analyze my bam file...it just can not get started. Here is what I did: ./bam-readcount/bin/bam-readcount -f hg19.fa -l site_list case.bam> ./case.rc The "site_list" file looks like this: chr1 9995 9995...the error: Minimum mapping qua…

bam-readcount

updated 6.9 years ago • sunyan727

Hi, I am using the great tools bam-readcount (which I really like), but I am having a problem, when I run the tool I got nothing as an output. I successfully install...the program, and I was able to use it on a set of bam file creating by bowtie2. Here is the cmd line. $ bam-readcount -l position.tab -w 1 -f mygenome.fna myBowtie2BamFile.bam Then...when I use Bam files coming from segemehl (…

software error alignment bam-readcount

updated 8.1 years ago • daron.6

I have installed bam-readcount using git clone --recursive as per the instructions on github. I am now using the command below to obtain read-count...metrics bam-readcount -q 1 -b 20 -f reference.fasta -l varScan.variants BAM_FILE >varScan.variants.readcounts However, I get an empty...output with a message Expect library: SX215 in BAM My bam file has the @RG field (tab-delimited)…

updated 10.2 years ago • tayebwajb

find somatic mutations in multiple tumor samples (to be used in clonality analysis). I don't get the readcounts if the caller did not identify a somatic mutation in a sample. I'm using bam-readcount to fill in the empty values...after merging Mutect results from different samples. Where I have values from both tools, the readcounts are lower in the Mutect results. Is there a way to use bam-readco…

bam-readcount

updated 7.0 years ago • sey

I have encountered similar questions elsewhere, but none exactly replicate my problem. I ran bam-readcount for about 1000 sites (across all chromosomes) for two samples from the same individual. I know both bam files have...by multiple somatic callers (mutect, varscan, etc). Yet, for one sample I get an empty output from bam-readcount, while for the other I get the expected counts. To illustra…

bam-readcount

updated 6.8 years ago • alexander.charney

Hi, I'm trying to run bam-readcount with region information (as a workaround to the 8000 read limitation). I use version 0.8 cloned from the repository...I run the alignment: bwa mem -t 8 reference_1.fa -p input.fastq | samtools sort -@8 -O BAM -o alignment_reference_1.bam - Output is indexed: samtools index alignment_reference_1.bam At this point, I need to...that contains one line…

bam-readcount bam

updated 5.8 years ago • obuzko

is A, the ALT is C and the position has 50 reads for A, and 23 reads for C. I am currently using [bam-readcount](https://github.com/genome/bam-readcount) for this purpose but I am little worried that my results might be skewed...I am note sure if ( because I did not find it in the documentation ) bam-readcount handles paired-end data. For example if two overlapping mates cover the base, and the…

RNA-Seq SNP

updated 5.8 years ago • chrys

Hello I'm using bam-readcount (version 0.7.4-unstable-35-0f3b356-dirty). Though it's version name doesn't exactly instill confidence, it is apparently...is that it is failing to report on a large swath of my 17738 bp reference sequence. As shown below, bam-readcount output skips from position 8062 to 13923. my_ref 8062 g 2 =:0:0.00:0.00:0.00:0:0:0.00:0.00 :0.00:0:0…

bam-readcount bam variant alignment

updated 7.7 years ago • mark.rose

Hi! I am analyzing bam files with more than 300,000 reads per site... But the maximum depth that the bam-readcount output reports is 8000. I saw a post

bam-readcount

updated 7.2 years ago • caritogandini

I am attempting to install bam-readcount on SLES 11. I am using cmake 2.8 and gcc 4.8.3. When I attempt to run make, I get the following: ``` BasicStat.cpp: In member...function 'void BasicStat::process_read(const bam_pileup1_t*)': /home/atkinja/installs/bam-readcount/src/lib/bamrc/BasicStat.cpp:101: error: cannot bind bitfield '((bam1_t*)base->bam_pileup1_t::b)->bam1_t::core.bam1…

bam-readcount software-error

updated 2.2 years ago • atkins.jackie

Hi, I am using the bam-readcount tool to compute the statistics of variants detected from NGS. I have one question. How is the "average position...average position of the variant is ~0.5. I also get similar number by looking at the MD tag of the bam file. But, bam-readcount provides 0.98 for that metric. For distance to 3', it provides 0.49. I am probably missing something

next-gen alignment bam-readcount

updated 7.8 years ago • rdas

filter) to remove false positives from the vcf files; however I stuck in the step of generating readcount from my vcf file. This is my command: bam-readcount -f hg38.fa -q 1 -b 20 -l all.Somatic.hc.var tumor.sorted.bam > all.Somatic.hc.readcount...I get this error: Minimum mapping quality is set to 1 [bam_index_load] fail to load BAM index. BAM indexing file is not a…

bam-readcount hc.readcount file BAM index

updated 5.4 years ago • Rahil

Hi all, I'm trying to run bam-readcount on a MacOS X 10.9.5 machine. I'm aware that bam-readcount returns a segfault when asked to process an entire bam...file, that's why I order it to run one chromosome at a time. Here's a example command I tried: bam-readcount -f 7Dref_all.fa 7dmerge_dedup.bam XV > 7dmerge_dedup_chrXV.readcount I get the following warnings, along...with an empt…

sequencing alignment

updated 2.2 years ago • damien.biotpelletier

I found bam-readcount to be very useful for further filtering SNVs and Indels. However, I do not understand a few fields of bam-readcount...and cannot find any other information regarding some of the fields other than the github page of bam-readcount. (1) num_q2_containing_reads → number of reads with q2 runs at the 3’ end (2) avg_distance_to_q2_start_in_q2_reads...length) to the start of the q…

snp sequence next-gen sequencing

updated 7.2 years ago • gongchangzhaojie

What kind of preprocessing do you need to use bam-readcount and fpfilter.pl for indels? This question has been already asked couple of times but so far I haven't found any...files contain somatic indels occuring in tumor samples. I am trying to filter these indels by using bam-readcount and fpfilte.pl. The format of VCF file is following; #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL…

bam-readcount indel fpfilter.pl VarScan

updated 7.5 years ago • Jokhe

of VarScan2 and SomaticSniper to filter my variants, but first I need to run another analysis on the bam file using bam-reacount. I'm having trouble installing bam-readcount because I don't have sudo access. I have installed things...dev But I get an invalid syntax warning about a python script. Can anyone help me install bam-readcount without sudo access so I can use the fpfilter.pl script? …

next-gen bam-readcount fpfilter.pl

updated 23 months ago • t2

pmc/articles/PMC4278659/). The recommendations are: Obtain metrics for the list of variants: bam-readcount –q 1 –b 20 –f reference.fasta –l varScan.variants BAM_FILE> varScan.variants.readcounts When trying to perform...the command line: bam-readcount –q 1 –b 20 –f hg38_genome.fa –l sample.varScan.snp.filter bqsr_output.bam > varScan.variants.readcounts...Minimum mapping…

bam-readcount BAM

updated 13 months ago • vanessagpds

the question title is self explanatory. Is it possible to output bases with zero coverage using [bam-readcount][1] tool. Something similar to `samtools depth`: Usage: samtools depth [options] in1.bam [in2.bam [...]] Options: -a output...all positions (including zero depth) [1]: https://github.com/genome/bam-readcount

bam-readcount

updated 7.0 years ago • user230613

Hi, I am running bam-readcount on a bam file and getting the following warning message: WARNING: In read WB85V:02305:02971: Couldn't find the generated

software

updated 8.1 years ago • tirza.doniger

After reading the documentation at https://github.com/genome/bam-readcount/blob/master/README.textile there is one column in the output from bam-readcount that I still don't understand...Columns 1-4 are chromosome, position, reference base, readcount. Columns 6-9 are colon separated values reflecting counts and quality metrics for reads with A, C, G, T, and ambiguous

samtools

updated 10.6 years ago • merbergd

Then, i get output.base.snp.Somatic.hc.filter Then to execute False Positive Filter: **bam-readcount -q 1 -b 20 -f reference.fasta -l output.base.snp.Somatic.hc.filter tumorfile.bam >varscan.variants.readcounts...but the output give me **Expect Library: LB in BAM** what is wrong? , i can't understand what should i input after " -l

snp sequencing varscan bam-readcount

updated 5.1 years ago • 9521ljh

Hi, I am using bam-readcount to calculate the read counts for each base in a list of genomic positions. However, in most of the samples some...any case all the positions defined in the bed file? At the moment I am using the following command: bam-readcount -f [ref-file] -l [bed-file] [input-file] Thank you

SNP

updated 7.6 years ago • jml96

Hi all, I am using bam-readcount to find reads in a RNA seq bam at the location of variants found using RNA seq. However, I am not able to get the right...output from all regions of my bam-file. For example: I am working with mm10, and I use the following command: bam-readcount -w 1 -b 20 -q 1 -f /mnt/storage/ref_fasta/Mus_musculus.GRCm38.dna.primary_assembly.fa...chr:start-stop] 1) For my C&…

RNA-Seq

updated 7.0 years ago • nils.rudqvist

No CMAKE_BUILD_TYPE specified, defaulting to release Extracting boost from /home/user/lib/bam-readcount_master/bam-readcount/vendor/boost-1.55-bamrc.tar.gz Boost build log can be found at /home/user/lib/bam-readcount_master...Configuring done -- Generating done -- Build files have been written to: /home/user/lib/bam-readcount_master $ make ... Scanning dependencie…

bam-readcount

updated 7.8 years ago • user31888

Hello, I have installed cmake on my MAC and was trying to compile bam-readcount but ran into an error: What I did, as sugested in the bam-readcount website, is: - first create a directory - entered...it - tried to compile it using cmake: cmake ../bam-readcount/ That's when I ran into this error: -- The C compiler identification is AppleClang 7.3.0.7030031 -- The CXX compiler

bam-readcount cmake

updated 7.9 years ago • matthieudelcourt

Hi! I'm trying to compile bam-readcount on SUSE Linux (without root rights, this is our cluster). I seem to have a problem with Boost, I get a bunch of errors

updated 10.4 years ago • Shellfishgene

I am now trying to run bam-readcounts. The sample I use is from human. But it takes almost 2-3 days to run one bam file. Is it normal? The size of my file is

bam-readcounts

updated 4.8 years ago • Laven9

to limit the base-quality-score to phred 13 (similar to default of samtools mpileup (1.3.1)), using bam-readcount (0.8.0). Despite various command modifications, I'm not getting the expected output. Default: bam-readcount -f human_g1k_v37.hotspot.fasta...0:0.00:0.00:0.00 -C:3:60.00:0.00:0.00:2:1:0.18:0.01:9.33:2:0.86:124.00:0.58 min-base-quality 13: bam-readcount -f human_g1k_v37.ho…

bam-readcount mpileup

updated 7.2 years ago • sheenams

Hey everyone! I'm receiving an error when I try to install Bam-readcount v1.0.1 on linux (centos7) with gcc 12.2.0 This is the error I receive in make If anyone of you can help fix this, I

bam-readcount

updated 13 months ago • shreshta2396

is an example of the sequencing output. As was suggested, I should filter the variants based on the bam readcounts (or read depth or allelic depth?). I'm confused of the definition and the discrimination among these three terms...Is the bam readcounts the same as AD or DP? Can anyone tell me the difference and which one should I use to filter the variants? Thanks

bam vcf sequencing genotype

updated 3.1 years ago • lincaijin1994

When running bam-readcount I get (minus the 8M previous warnings of the same type): WARNING: In read m151222_205817_42179_c100908792550000001823210904291644_s1_p0

bam-readcount bam

updated 7.9 years ago • mark.rose

Hi I'm using bam-readcount to get coverage per nucleotide as part of our exome-seq variant annotation pipeline, following bwa and gatk...when i run bam-readcount, i get the following error for each position: "Couldn't grab single-end mapping quality for read HWUSI-EAS753:41...FC:4:79:2401:16705. Check to see if SM tag is in BAM" Is there a way to overcome this error? Thanks

updated 11.0 years ago • amnonim

calling by using additional fpfilter.pl tool. This tool, in turn, requires read counts generated by bam-readcount tool. This is the step where I'm having a frustrating problem. I have paired-end sequencing data in FASTQ format...and I have aligned it by using BWA-MEM without any errors, Generated SAM file is then converted into BAM format by using Samtools (v. 1.3.1.) with following commands; …

bam-readcount Samtools EOF-marker

updated 7.7 years ago • Jokhe

Dear All, When I use bam-readcount to count each SNP position's depth for making %VAF, Especially for those pair samples, only happened mutation...variants.positions_sorted.bed > variants.positions_sorted.bed #Step three: #Example: bam-readcount -b 15 -q 15 -w 1 \ -f reference/Mus_musculus.fa \ -l variants.positions_sorted.bed \ /bam_files/$1.bam \ &…

SNP sciclone LOH sequencing bam-readcount

updated 6.5 years ago • Haitao

Hi all, For any given SNP, is there any tools can be used to calculate the F1R2 and F2R1 readcount in a relevant bam file? Thanks. Ming

sequencing next-gen

updated 6.2 years ago • xie, ming

I am having trouble installing bam-readcount on centos 5 using Cmake 3.0.2 due to a boost library linking error. Since boost 1.55 is installed system wide

bam-readcount software install

updated 2.1 years ago • oscarjiao

line 210, in remap_bwamem_bam raise ValueError("ERROR\t" + now() + "\t" + mutid + "\tbam readcount < fastq readcount, alignment sanity check failed!\n") ValueError: ERROR 2017-07-06 09:03:39.933970 haplo_chr1_27691816_27691816...bam readcount < fastq readcount, alignment sanity check failed! This error report does not appear all the time, but about one

software error genome

updated 6.8 years ago • jing.mengrabbit

Dear, I painfully discovered that he tutorial using bam-readcount in the CurrProtBioiunfo Varscan 2013 paper is not correct and that one cannot use varscan results but needs...of -l to load Varscan native data (not VCF) directly and adapt the coordinates on the fly inside bam-readcount to produce the correct footprint? Thanks in advance Stephane [1]: https://www.biostars.org/p/93418

varscan2

updated 6.5 years ago • Stephane Plaisance

When I run bam-readcount with a site-list file containing only one line, a start..stop span of 21 bases, it produces the expected output, with...for the midpoint base DOES NOT include a status for bases -AA. Why would this happen? The same bam file and same reference file are used in each case. Why wouldn't it be repeatable? I do not know what version of bam-readcount

software error

updated 8.0 years ago • twtoal

Hi all, I have a question on how bam-readcount calculates the "average mismatch quality sum": Assume there are 3 aligned reads (with length 100) at a locus, read1

quality

updated 11.0 years ago • mrfox

Hi, I'm running bam-readcount (commit `6c3f3ae901`) on a few hundred bam files against a single reference fasta file (designated with `-f`). However

bam-readcount

updated 2.6 years ago • Chris F.

BiocManager::install("HMMcopy") library("HMMcopy") While trying to run HMMCopy readcounter in R, I am not able to see its module **readcounter**. readCounter** Error: object 'readCounter' not found I need your help

readcounter ichorCNA CNV HMMcopy

updated 2.8 years ago • shivangi.agarwal800

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