Missing contigs in BAM files

Illumina / strelka

Strelka2 germline and somatic small variant caller

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Missing contigs in BAM files #4

Open mingyi-wang opened 7 years ago

mingyi-wang commented 7 years ago

I tried to run configureStrelkaSomaticWorkflow.py for the WGS BAM files. But got an error: CONFIGURATION ERROR: 'normal' BAM/CRAM file is missing reference fasta chromosome: 'hs37d5' I guess that the BAM header exclude the decoy sequence. How to work around this issue?

Thanks,

ctsa commented 7 years ago

The reference sequence must match the BAM header reference information, and all BAMs must match each other.

The solution is to use the same reference sequence used to map the input BAM alignments.