I cannot extract all of the contents of a gzipped vcf file. The file is part of an encrypted tarball I downloaded from dbGaP. After decryption, I was able to extract a directory of files with this command:

 tar -xvf phg001.tar

When I used Plink to convert one of the extracted vcf files to a bed file, I got an error message: Error: Line 20 of .vcf file has fewer tokens than expected.

I counted the number of lines in the files with the help of zcat.

zcat chr22-filtered.dose.vcf.gz | wc -l

Output:

gzip: chr22-filtered.dose.vcf.gz: decompression OK, trailing garbage ignored
19

And if I try to unzip the file, I get a similar message about trailing garbage.

gzip: test22.vcf.gz: decompression OK, trailing garbage ignored

The file is too large to have only 20 lines, and if I count the number of lines without using zcat, there is indeed more to the file.

wc -l chr22-filtered.dose.vcf.gz
3632730 chr22-filtered.dose.vcf.gz

How can I extract all of the contents of the zipped file.

All advice is appreciated.
Paul