<p>I want to process the <a href='http://samtools.sourceforge.net/SAM1.pdf'>sam</a> file created by <a href='http://bio-bwa.sourceforge.net/'>BWA</a>, if it is sorted by the sequence coordinate on reference, it will be …
<p>I use picard tools to take a <a href='http://bio-bwa.sourceforge.net/'>BWA</a> alignment <a href='http://samtools.sourceforge.net/SAM1.pdf'>sam</a> file and convert it into a sorted <a href='http://samtools.sourceforge.net/SAM1.pdf'>bam</a> file. Normally this works …
<p>Dear Biostars</p> <p>I am aware of <a href='http://samtools.sourceforge.net/'>samtools</a> splitting of <a href='http://samtools.sourceforge.net/SAM1.pdf'>bam</a> file based on chromosome. But is there any way I can divide a …
<p>Hello,</p> <p>I was looking into filtering our Sniper calls using the included perl scrips in order to look at certain mapping quality and somatic score …
<p>Hi, I was hoping to compile somatic-sniper but I received some issues:</p> <pre><code>$ make Scanning dependencies of target sniper [ 10%] Building C object build/src/lib/sniper/CMakeFiles/sniper.dir/allele_util.c.o …
<p>Hi,</p> <p>I have a tumor sample with me, which has a blood normal and solid normal. I'm using <code>MuTect</code> to generate variants. I wanted to …
<p>Does denovogear support marked dup and sorted <a href='http://samtools.sourceforge.net/SAM1.pdf'>bam</a> files? I was trying to run the bcf file generated from mpileup command on the marked …
<p>Hi for running the <a href='http://samtools.sourceforge.net/SAM1.pdf'>bam</a> file through somatic sniper, do we need a marked duplicate <a href='http://samtools.sourceforge.net/SAM1.pdf'>bam</a> file? Thanks</p>
<p>Hi!</p> <p>I have three aligned pair end reads in <a href='http://samtools.sourceforge.net/SAM1.pdf'>BAM</a> format. Two of them are of same sample run in different lanes. I first …
<p>I converted the output of soap2 which is map file to <a href='http://samtools.sourceforge.net/SAM1.pdf'>sam</a> file using map2sam.pl and then converted this <a href='http://samtools.sourceforge.net/SAM1.pdf'>sam</a> to <a href='http://samtools.sourceforge.net/SAM1.pdf'>bam</a> …