Question: CNV calling by using mrsFAST as mapper
gravatar for ManoloS7
11 months ago by
ManoloS70 wrote:

Hi all,

I have different paired-end exome sequencing samples and I would like to call CNVs for them using CoNIFER ( Previously, I have to map my samples, and the developer recommends mrsFAST.

  1. First of all, I have read ( that, for calling CNVs, you do not want to use the paired-end mode of the program, but I still do not see clearly why should not I. Any ideas?

  2. On the other hand, I have noticed that mrsFAST cannot handle reads with irregular lenght. Am I right? I had to use the --crop command to cut them and make them the same lenght.

  3. I am not sure if I am doing everything OK. After creating my bam files, I use CoNIFER to call variants (by creating the RPKM files and the .hdf5 file needed) but I do not see what I expected. In fact, there is a duplication that we have previously seen by experimental techniques that does not appear, so I am afraid that I am missing something and that I messed it up somewhere.

This is my command:

mrsfast --search $hg19 --seq $input/S${i}_R1.fastq${a} --seq $input/S${i}_R2.fastq${a} --mem 25 --crop 130 -o $bams/S${i}_${a}.sam

Any ideas and comments are welcome. :)

Thank you in advance.

alignment next-gen • 237 views
ADD COMMENTlink written 11 months ago by ManoloS70
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1671 users visited in the last hour