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Problem with Indel Target Realigner, extra contig added?
I run into a problem after the pre-processing, it seems that extra contigs where added to my bam file compared to the reference I used, which make the indel realigner step impossible to do. I have checked the headers of my file and the reference is the same but my bam file as a hundreds of additional contigs. Not sure what happen.
The steps to get the bam where:
- Aligned with bwa mem
- Transform to bam and sort (Samtools)
- Dedup (picard)
- Add read group (picard)
- Index bam (samtools)
- Run Realigner target creator
When I check the header of my bam file it still show the right contigs but when running it complains of difference (additional) compare to my reference. I am currently re-testing the whole pipeline on a single sample but if you have any pointer to what could cause this, maybe a problem with the bam formating?
I am running GATK 3.3.0-g37228af
I have attached the ouput log from the command.
PS: I attended your workshop in Cambridge!