Hi everybody,
A bam file has been aligned using hg19 reference genome. Thus, the chromosome notation is [chrM, chr1, chr2, chr3, chr4, ..., chrX,chrY].
I want to look for PMs using MuTect that requires in input vcf files from dbSNP and COSMIC. In these vcf files the chromosome notation is [1,2,3,4,...,MT,X,Y] according to b37 notation.
a) As expected running MuTect on these files, it returns the error:
##### ERROR MESSAGE: Input files dbsnp and reference have incompatible contigs: No overlapping contigs found.
b) I succesfully reheader bam file in order to remove 'chr' and changing chrM to MT, but the error now is:
##### ERROR MESSAGE: Input files reads and reference have incompatible contigs: Found contigs with the same name but different lengths:
##### ERROR contig reads = MT / 16571
##### ERROR contig reference = MT / 16569.
c) The last attempt was to add 'chr' and replace chrM to dbSNP and COSMIC vcf files required by MuTect. Error is:
##### ERROR MESSAGE: Invalid command line: No tribble type was provided on the command line and the type of the file could not be determined dynamically.
How can I run MuTect on these bam and vcf files?
many thanks
Allegedly there's an hg19 to b37 liftOver file provided by GATK in the resource bundle. If nothing else, just use that and call it done (I imagine that'll take a while to run).
Devon, you should put this as the answer so Nicolas can accept it.