I have been trying to convert bcf and vcf files back and forth with bcftools for testing purposes. So, first I ran a basic samtools mpileup on Galaxy, resulting in "test.bcf". After converting this file back to vcf in Galaxy, reconverting it to bcf did not work, so I downloaded the file and tried it "the basic way" on the command line.
Trying this works fine and produces a perfectly normal looking vcf file (it also works in Galaxy):
bcftools view test.bcf > test.vcf ##fileformat=VCFv4.1 ##samtoolsVersion=0.1.18 (r982:295) #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT path/to/test.dat chrTest 420 . N T,X 0 . DP=1;I16=0,0,1,0,0,0,71,5041,0,0,42,1764,0,0,0,0 PL 42,3,0,42,3,42 chrTest 421 . N C,X 0 . DP=1;I16=0,0,1,0,0,0,71,5041,0,0,42,1764,0,0,1,1 PL 42,3,0,42,3,42 chrTest 422 . N T,X 0 . DP=1;I16=0,0,1,0,0,0,71,5041,0,0,42,1764,0,0,2,4 PL 42,3,0,42,3,42 chrTest 423 . N A,X 0 . DP=1;I16=0,0,1,0,0,0,71,5041,0,0,42,1764,0,0,3,9 PL 42,3,0,42,3,42
Then I went on converting test.vcf back to test.re.bcf.
bcftools view -b test.vcf > test.re.bcf [bcf_sync] incorrect number of fields (0 != 5) at 0:0
I thought the error was caused by the header and produced a version of test.vcf without the first two and one without any header lines. Still the same error message.
I have seen the same error (incorrect number of fields) a lot in other forum posts and such, but what puzzles me here is the fact, that the first conversion from bcf to vcf is working and producing normal output, but obviously bcftools cannot cope with the type of vcf it has produced itself. Has anyone else experienced this and maybe found a reason and a solution for this problem?