several warnings: Use of uninitialized value, Use of uninitialized value in join or string

[corneliabuus]

I have a problem when trying to run VarDict on phage data. It gives a lot of the same errors, for what looks like every line in our bam,bed or fasta file. I've tried to looking into every file and made sure they are indexed, but we can't seem to find a problem.

[PolinaBevad]

Hi @corneliabuus , Sorry that you have a problem!

What version of VarDict do you use? It seems that it is not the last one (1.6.0 or master branch version). I recommend trying to upgrade it to the master branch version first. Also, can you please provide a command line with options that you use when running VarDict?

[corneliabuus]

We just cloned it, with the following: git clone --recursive https://github.com/AstraZeneca-NGS/VarDict, so I think it's the latest.

our command line look like this:

!/bin/bash

AF_THR="0.01" # minimum allele frequency

VarDict/vardict -G NC_007019.1.fa -f $AF_THR -N W1T1 -b W1T1.sorted.bam -c 1 -S 2 -E 3 -g 4 W1T1.bed | VarDict/teststrandbias.R | VarDict/var2vcf_valid.pl -N W1T1 -E -f $AF_THR > W1T1.vcf

[PolinaBevad]

Okay, thank you for checking! Can you please provide a small slice of your BAM file where it is reproduced so I can check what is the problem?

[corneliabuus]

Yes thank you for helping. I've sendt you a mail with a picture of a slice of the bam file.

[PolinaBevad]

As we discussed in emails, the reason was incorrect locale, which can cause problems in both versions. Thank you, I'll close the issue!