Clipping and trimming with MrFast (for eventual CNV discovery)

[legaultm]

In the mrFAST manual, it says:

NOTE: mrFAST will assume that the read lengths are uniform within a file (paired-ends may differ from each other). If the lengths of the reads are not the same in a file, it may crash or output incorrectly formatted SAM files.

Since my sequencing pipelines trims and clips the fastq files by using the fastq-mcf utility, the sequences will not be completely uniform in length. I was wondering if MrFast only worked on raw, untrimmed and unclipped data, or if this particular pre-processing step was acceptable for use with mrFAST.

[legaultm]

So to anyone who might still be interested. After some testing, I did get a Segmentation fault when using trimmed/clipped reads. Thus, I considered two different options.

1. Use the clip/trim data, but remove additional bases at the end of reads to make the length uniform (and discard the reads that are too short for this process).

2. Use the raw reads.

I chose to use the raw reads, since for CNV calling the low quality bases at the end of the sequences shouldn't be too problematic. Also, I figured the mapping quality shouldn't be affected in a very significant manner.