Error when unzipping .gz files from GATK?

Question

[vctrm67]

Posting here because it seems to get a faster response. I get this error when trying to do gunzip /vcf.gz of the output of HaplotypeCaller:

gzip: /file: invalid compressed data--crc error

gzip: /file: invalid compressed data--length error

Anyone know what might be wrong? I double checked and they are indeed .gz files.

Answer 1

[Ram]

Are you sure the file /vcf.gz exists? / is the root directory. Do you mean to uncompress ./vcf.gz?

[vctrm67]

Yes, that is what I meant.