compression of FASTQ files

Question

[kshah.bch]

I want to merge fastq files of the same sample sequence in two different times, one file is .gz and the second is .qp. I did merge them with cat file1.gz file2.gz file3.gz > allfiles.gz and the out file is either .qp or .gz. However, analysis of this data with mutect show a problem "Input file is not a quip file". What is the best out put file format which can be analyzed with mutect in this case?

Answer 1

[ATpoint]

Fastq should be gzipped, that's the standard. Whatever qp is, decompress and recompress with gzip and be done with it. Don't overthink it.

[kshah.bch]

Thank you Dear. I am new to working on HPS and linux. I want to decompress the fastq.qp files but i don't have a command for this to do it in HPC.

[GenoMax]

Can you post the output of file fastq.qp command?

It is possible that the file name contains a tyopgraphic error and the file actually is gzipped.

You can uncompress gzipped files in many ways (SEE). That said many programs will accept gzipped files so you don't need to decompress them first.

[kshah.bch]

fastq.qp is compressed file processed with quip tool. I solved the problem with the help of another expert. Thank you for guidance.