Hi,

I am running covert2annovar.pl in Annovar to change .vcf files from Mutect output to .vcf files that used in Annovar. command as below:

convert2annovar.pl -format vcf4 -filter pass -allsample $f -outfile $f".avinput" &

I got right results last time, as this:

chr1    1385923 1385923 A       G       0.5     .       2
chr1    1385926 1385926 A       C       0.5     .       2
chr1    1385941 1385941 T       A       0.5     .       2

but this time, I got this:

chr1                                    .       .
chr1                                    .       .
chr1                                    .       .

I double checked the input files and parameters, which are the same as last time.

Could anyone help me to figure out where the problem is? Thanks.