Questions tagged [bwa]

bwa (Burrows-Wheeler Aligner) is a software for aligning reads obtained with Next Generation Sequencing.

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89 views

Trying to create a .bam file without the need for a .sam file

I'm trying to use the code specified in this link to create a .bam file without the need for a .sam file. Here is the code I'm using: ...
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Why does the ENCODE chip-seq pipeline discards reads with a hard-clipped alignment?

Hard-clipped alignments are alignments in which one or both the ends are clipped AND map to other genomic coordinates. As you may know, BWA-MEM reports hard-clipped alignments as supplementary. ENCODE'...
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BWA doesn't recognize HiC options

I'm trying to run bwa on HiC data. This is the command I'm giving: bwa mem -5SP -T0 -t4 -R '@RG\tID:\tSM:\tLB:\tPL:ILLUMINA\tPU:none' REFERENCE.fa PAIR1.fq PAIR2.fq ...
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253 views

Samtools Index: Chromosome Blocks not Continuous

I am working with short-read whole-genome sequences from the NCBI's SRA. I have aligned and sorted all of my short-read sequences and am attempting to index each sequence into .bai format using ...
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1answer
37 views

BWA: Detecting Variation between Reference Genome and Short-Read Sequences

I need to identify all loci in the short-read sequence at which the number of microsatellite repeats (i.e. number of copies of "AA," "GTC," etc.) differ from the reference genome, ...
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1answer
104 views

How to extract unmatched reads using bwa and samtools?

I have a single read (NOT paired) that I need to pass through the workflow described in Beauclair et al. paper (free version here https://rnajournal.cshlp.org/content/24/10/1285.long) for identifying ...
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1answer
46 views

How can I get unmatched reads for defective genomes analysis using bwa and samtools?

I am trying to follow the Beauclair et al. paper (free version here https://rnajournal.cshlp.org/content/24/10/1285.long) for identifying defective genomes using their DI-tector program. According to ...
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1answer
40 views

No MQ tags in VCF files

To call minority variants in my Mtb sequences I'm using a pipeline of ...
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bwt suffix array construction

I found a very good link to generate bwt suffix array in BW based tools. @user172818 provides a nice code. could anyone tell me how to store SA elements' original position in the original string?
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Variant calling for a subset of genes using whole gneome sequencing data

I have few 100 raw fastq files from whole-genome sequencing data and I would like to map these files to a set of genes only (and not whole genome) so as to find SNP's associated with them. Can anyone ...
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What is the meaning of the “*” character in bwa fastmap's output?

I am mapping kmers back to a few bacterial genomes using bwa fastmap: ...
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Is BWT based aligner suitable for any types of alignment task?

Burrows wheeler transformation based aligner like BWA or bowtie seems a standard alignment tool used many area. I was just wondering if there is a kind of alignment task in which BWT algorithm is not ...
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259 views

Error with BWA Mem input having multiple fastq files using cat and process substitution

Running BWA Mem on a number of paired end fastq files using process substitution on the inputs results in this error: ...
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How to map multiple CDS sequences to exome data using bwa mem?

Normally, I use bwa-mem to map my fastq reads for a bunch of species using one protein-coding gene CDS from my reference species. This was fine when I had to try it for just a group of genes...I would ...
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1answer
103 views

How to take into account alternative bwa mem mapping when computing coverage

when mapping short reads with bwa mem, if a read has alternative mapping positions they are reported by bwa mem in the X0 and XA tags. Now, let's say I want to compute the coverage of my bam file. ...
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181 views

Proper use of BWA MEM on multiplexed GBS sample

I have a multiplexed lane of GBS sequencing reads as a fastq file. I understand the first step is to demultiplex and trim the adapter sequences from the reads. This yields many individual fastq ...
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1answer
820 views

samtools view: writing to standard output failed: Broken pipe

I have the following alignment script which uses BWA: ...
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1answer
78 views

Determining Read Groups

Which Read Groups are correct: ...
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346 views

How to output all sequences with bwa mem, not `*`?

I've been running bwa mem -a for alignment, using the -a flag---this will output all alignments for SE or unpaired PE I've ...
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561 views

What is mate rescue in bwa mem?

BWA mem has the -S and -P tags for skip mate rescue and skip pairing; mate rescue performed unless -S also in use. What do ...
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Sequence alignment using BWT

My Problem: Skipping some specific background, what I want to do is judging whether some soft-clipping sequences are the same, which may result by the same SV event. Colored bases in Fig.1 is an ...
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763 views

What is the correct way to map Hi-C data with bwa mem?

Library Prep I have a Hi-C library prepped using an enzyme that cuts at GATC, so it leaves GATCGATC as the junction sequences. ...
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2answers
93 views

How to map reads shorter than 32bp with minimap2?

I mapped fasta sequences to a reference. The fasta sequences range in length from 17bp up to several hundred bp. I used minimap2 with the following command: ...
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1answer
109 views

Minimap2 -ax map-pb doesn't output tlen field

I have used minimap2 to map some pacbio reads to a reference genome. I would like to know the "insert size" (true length of sequence) relative to the reference. More specifically, I want to know the ...
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261 views

How to read .bwt file .sa file?

In BWA project in bwt.c file I found bwt_dump_bwt method and bwt_dump_sa method. I want to use them to read .bwt file and .sa file. I wrote the following program: ...
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375 views

How BWA generate index files?

I need to know how BWA generate bw and sa in less memory usage ? Do they save all rotations temporary ? I need to know do BWA stores all rotations so that it can sort the rotations alphabetically ? ...
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1answer
202 views

Generating burrows-wheeler-transform and a suffix array of a DNA sequence with less memory

Also posted on biostars After indexing bwa index -a bwtsw reference.fa I got files. like .bwt file and .sa file. The naive way of generating these file is:   ...
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How does Li and Durbin's BWA paper compare alignment programs on real data?

Li and Durbin's "Fast and accurate short read alignment with burrows-whleeler transform" found here, says: We evaluate the performance of BWA on ... real paired-end data by checking the fraction ...
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418 views

Interpreting 0x200 flag in bwa-mem alignments

I am looking at the bwamem.h code in http://github.com/lh3/bwa and found that BWA-MEM will give flag 0x200 to what it calls ...
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1answer
2k views

Is there a more elegant solution to the bwa-mem: paired reads have different names error?

I'm currently trying to run bwa-mem on Influenza substrains using the following command: ~/bwa mem h5n1_1_cons.fa h5n1_1_read1.fq h5n1_1_read2.fq h5n1_1_cons.fa ...
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1answer
1k views

Estimating BAM file from compressed fastq file size

Is there a way to estimate the size of a BAM file will have after mapping with BWA? The input file are two mates fastq files, compressed with gzip, each one about 70G.
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1answer
331 views

Mark BWA-SW split alignments in output for long reads

Is there a way to remove split alignments of single-end long reads from BWA-SW output? BWA-MEM has an option to include or flag split alignments in the result, but it seems BWA-SW method include them ...
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2answers
7k views

Meaning of BWA-MEM MAPQ scores

Does anyone know what the MAPQ values produced by BWA-MEM mean? I'm looking for something similar to what Keith Bradnam ...
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2answers
557 views

Problems to Extract uniquely mapping reads from BWA MEM alignment

I did a mapping of genomic paired-end reads to a reference assembly using bwa mem. I need to extract the reads that mapped only once to my reference. For that, I have tried to follow the method ...
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2answers
7k views

Obtaining uniquely mapped reads from BWA mem alignment

This is based on a question from betsy.s.collins on BioStars. The original post can be found here. Does anyone have any suggestions for other tags or filtering steps on BWA-generated BAM files that ...
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4answers
459 views

Library for computing BWT-based alignments

I am writing a software tool to which I would like to add the ability to compute alignments using the efficient Burrows-Wheeler Transform (BWT) approach made popular by tools such as BWA and Bowtie. ...
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1answer
3k views

Why is bwa-mem the standard algorithm when using bwa?

The industry standard for aligning short reads seems to be bwa-mem. However, in my tests I have seen that using bwa backtrack (bwa-aln + bwa-sampe + bwa-samse) performs better. It is slightly slower, ...
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1answer
159 views

Do you use SNAP for short-read mapping?

I am calling SNPs from WGS samples produced at my lab. I am currently using bwa-mem for mapping Illumina reads as it is recommended by GATK best practice. However, bwa is a bit slow. I heard from my ...
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275 views

Why most aligners do not output the “X” CIGAR operation?

As I read the SAM spec, the "X" CIGAR operator represents a mismatch. This seems useful as we can know where are the mismatches without looking at the reference genome. However, many popular aligners ...
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863 views

What are all the reference files produced by bwa index, and are these dependent upon whether the reference is zipped?

I have indexed a gzipped reference with bwa: bwa index reference.fa.gz, which produces a series of other files ...
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1answer
2k views

How does the BWA-MEM algorithm assign its mapping qualities?

Is there any resource (paper, blogpost, Github gist, etc.) describing the BWA-MEM algorithm for assigning mapping qualities? I vaguely remember that I have somewhere seen a formula for SE reads, which ...
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2k views

Difference between BWA-backtrack and BWA-MEM

Many of my colleagues recommend I use BWA-MEM instead of regular old BWA. The problem is I don't understand why and reading the BWA man page doesn't seem to help the matter. What is the difference ...