SNVer error on pooled sample

[Anelda]

Hi there,

I'm running SNVer 0.2.0 on Mac OS x 10.6.8.

The input is a bam file generated from Ion Torrent data - Torrent server v1.5.

The reference is a single gene (5KB) and the samples that were sequenced and mapped are 50 pooled individuals (1 bam file).

When I run it with the command below, I get the following error:

java -jar SNVerPool.jar -i input_bam -r reference_file -c pool_info_file -o output_snver

Ready for Pool Pileup...
Input Bam Directory is : input_bam/
Output Result File is : output_snver.raw.vcf
net.sf.picard.PicardException: Requesting earlier reference sequence: -1 < 0

The thread here suggested sorting the bam file, but mine is sorted?

Any suggestions on how to solve this will be great.

The average coverage is ~2500X if that may be the cause of the problem?

Thanks!

Anelda

[wang]

From SNVer Manual:
-r Reference file must be the same as what are used in the input
bam files. Inconsistent reference file, such as different chromosome
names and different chromosome length, will prevent SNVer from
running.

Hope it helps,