mrsFASTA and conifer

Question

[kristincilla_16]

Hi,

I am trying to use CONIFER to analyze copy number variation in target sequencing. I had an error with my bam file. I think that it was because I have to use mrsFASTA to align my .fastq files. But when I am trying to use mrsFASTA, it gives me another error, and I think that it is because reads have to had the same length. Does somebody know if mrsFASTA works with reads with different length?

Thanks,