<p>Hello</p> <p>I want to align my reads to the reference genome and then use GATK for downstream analysis. I am using <a href='http://bio-bwa.sourceforge.net/'>bwa</a> mem protocol.</p> …

<p>I have dataset which is exome-seq, and I am planing to use <a href='http://bio-bwa.sourceforge.net/'>bwa</a> aln for alignment with its default values, and use the GATK …

<p>I want to get uniquely mapped reads from <a href='http://samtools.sourceforge.net/SAM1.pdf'>bam</a> files aligned with <a href='http://bio-bwa.sourceforge.net/'>bwa</a>-mem using the -M option (to make it compatible with picard-tools). …

<p>Hello,</p> <p>I have a dataset of short reads in which some fastq files are in the Illumina 1.5 format, and others in the Illumina 1.8. …

<p>Can any one help me please I want use <a href='http://bio-bwa.sourceforge.net/'>BWA</a> aligner, when I downloaded I cd into the file and made it and it …

<p>This question is a follow up from: <a href='/p/70597/'>Are some sequences uniquely mapped by BWA when mapped as paired-end that would not be when mapped …

<p>I want to switch from using <a href='http://bio-bwa.sourceforge.net/'>bwa</a> aln+sampe to <a href='http://bio-bwa.sourceforge.net/'>bwa</a>-mem, but I notice that there is no quality soft-trimming in the latter. (It …

<p>Hi,</p> <p>I just aligned several exome samples with <a href='http://bio-bwa.sourceforge.net/'>bwa</a> mem and then processed the output through several pipeline steps. This is the first time …

<p>Hello</p> <p>I am unsure how best to use <a href='http://bio-bwa.sourceforge.net/'>BWA</a> on two files containing haplotypes of an exome. There are three <a href='http://bio-bwa.sourceforge.net/'>BWA</a> types. I …

<p>Hi all, </p> <p>Could you please tell me how to integrate or use <a href='http://bio-bwa.sourceforge.net/'>bwa</a>-0.6.1-tpx.patch in <a href='http://bio-bwa.sourceforge.net/'>bwa</a> sampe ?</p> <p>Thanks Sara</p>