Can We Use Multiple Normal Bam Files As Input For Mutect To Generate Vcf Files?
Hi,
I have a tumor sample with me, which has a blood normal and solid normal. I'm using MuTect to generate variants. I wanted to know if I could use multiple normal BAM files as input for a particular tumor BAM file. Or should I use them separately?
<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>If I have a PCR free high coverage <a href='http://samtools.sourceforge.net/SAM1.pdf'>bam</a> and a low coverage <a href='http://samtools.sourceforge.net/SAM1.pdf'>bam</a> and I downsample the PCR free high coverage <a …
<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>I have two <a href='http://samtools.sourceforge.net/SAM1.pdf'>BAM</a> files that have a different sample in read group (@RG) section. I would like the sample to be the same. …
<p>Hi,</p> <p>I'm having trouble sorting a <a href='http://samtools.sourceforge.net/SAM1.pdf'>bam</a> file. I give the following command.</p> <pre><code>samtools sort -m 40G -o file.bam file.sorted </code></pre> <p>But I get …
<p>Is it possible in any way to run the somatic sniper with merged <a href='http://samtools.sourceforge.net/SAM1.pdf'>bam</a> file or do I always need to provide the tumor …
<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 have a <a href='http://samtools.sourceforge.net/SAM1.pdf'>BAM</a> file produced by <code>bowtie</code> with multiple alignments per read (<code>--all</code> option specified). Unfortunately, a tool I use which requires the …
<p>Hi, I am running <strong>Pindel version 0.2.4p, March 26 2012</strong>, on a set of <a href='http://samtools.sourceforge.net/SAM1.pdf'>BAM</a> files. It chokes on them, printing out:</p> <p><strong>No currentState.Reads …
<p>I have patient tumor/normal HiSeq paired end data. I have 2 <a href='http://samtools.sourceforge.net/SAM1.pdf'>bam</a> files which were cleaned/sorted/duplicates removed.One <a href='http://samtools.sourceforge.net/SAM1.pdf'>bam</a> for tumor and other for …