UnifiedGenotyper ERROR MESSAGE: Trying to clip before the start or after the end of a read

pylpyl Member
edited October 2012 in Ask the GATK team

Hi all,

I observe a curious behavior of the unified genotyper when using 2 bam files to create a VCF file with both samples.

It is an error with the message as shown in the subject, but it only occurs when I process two input bams at the same time (i.e. -I a.bam -I b.bam as parameters) and have -glm BOTH.

With both files and -glm SNP I get no error and with each file separately and -glm BOTH I also don't get the error, but with both files and -glm BOTH it occurs.

It must be the interplay between the two files that causes it and I think both files are valid since they both run fine without errors or warnings when used separately.

I just noticed that it happens when I use the ENSEMBL genome fasta with chromosomes 1..22 X and Y but not If I just give the respective chromosome (22 in this case), that's strange also.

Cheers,
Paul

p.s.: I use GATK 2.1-12 and specifically try to call position 22: (I narrowed it doen to this position as the offending one)

I can't upload sam or bam files with the reads causing the problem (it's only 14 respectively 49 reads), should I put them somewhere else? Like, the ftp server or so?

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