[Useq-users] STP and GATK

[Joseph W. <jos...@bi...>]

I'm having an issue running the GATK's RealignerTargetCreator on bam files generated using STP. I get the following error when I try to run the app:

##### ERROR MESSAGE: Input files reads and reference have incompatible contigs: Found contigs with the same name but different lengths:
##### ERROR   contig reads = chrI / 15172264
##### ERROR   contig reference = chrI / 15072423.
##### ERROR   reads contigs = [chrX, chrI, chrV, chrIII, chrIV, chrM, chrII]
##### ERROR   reference contigs = [chrI, chrII, chrIII, chrIV, chrM, chrV, chrX]

I saw in an earlier post that this error is caused by the bam file header having a different length than the reference fasta file. How would I change the header to fix this? Is the correct tool to use going to be picard ReplaceSamHeader.jar? Also, what are the appropriate values to change (i.e. should the length of each chr in the header be changed to match the length of each chr from the UCSC chr.fa)?

Thanks for the help,

Joe W