varFilter "Use of uninitialized value" problem

[Erka75]

Hi all,

I have a problem when trying to use samtools to generate a vcf file and to filter it.
I am new to this field and I ve been trying to use the simplest commands suggested in most tutorials:
samtools mpileup -vcf ...

First, I get these errors for the v and c options of mpileup
mpileup: invalid option -- 'v'
mpileup: invalid option -- 'c'
Which may or may not matter, I dont know. It seems the pileup file generated is lacking a header. Is this a problem for the filtering?

Then, if I want to filter the pileup file using samtools.pl I systematically obtain the following comment for every line :
Use of uninitialized value in numeric lt (<) at /usr/share/samtools/samtools.pl line 93, <> line 9998.

Thanks in advance!

[swbarnes2]

The second problem is because your mpileup is not right. Try redownloading samtools.